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"content": "\u003cp>I hesitatingly looked at the weather report the night before. I knew we might be in for it. No rain was forecast but the swell looked bigger than I hoped. So as the sun was rising over Pillar Point Harbor in Half Moon Bay, it was some trepidation that I sighed and boarded the fishing vessel Donna Kathleen. Morning coffees were passed out to those who wanted them and we cast off. As the plucky ship made its way beyond the break, I met with captain \u003ca href=\"http://artliveshere.org/profiles/tim_maricich_bio.html\">Tim Maricich\u003c/a>, the crew, and the two scientists we’d be profiling; Dirk Rosen from \u003ca href=\"http://www.maregroup.org/\">Marine Applied Research and Exploration\u003c/a>, the non-profit who builds and pilots the underwater remotely operated vehicles used to survey the sea floor, and Professor \u003ca href=\"http://sep.csumb.edu/staff/james/\">James Lindholm\u003c/a>, from the \u003ca href=\"http://sep.csumb.edu/ifame/index.php\">Institute of Applied Marine Ecology\u003c/a> at California State University Monterey Bay, who is in charge of chronicling and interpreting everything the ROV encounters. Their collective mission was to survey areas of the newly established Marine Protected Areas approximately 2 miles off the North-Central California coast.\u003c/p>\n\u003cp>\u003ca href=\"http://www.dfg.ca.gov/mlpa/\">Marine Protected Areas\u003c/a>, or “MPAs,” have recently been set aside up and down the coast of California. These are essentially restricted no-fishing zones that have been established to allow fish to breed and grow big with the idea that they will be able replenish State waters. This is different from the standard fishery management practices of the past in that it is aimed to protect entire ecosystems all of the time instead of managing one type of fish at certain times of the year.\u003c/p>\n\u003cp>The science seems to back up the theory. In other parts of the world, marine protected areas have shown success in fish populations growing in both number and size. In one case in Mexico, this type of program has been scientifically proven to be successful in bringing back big fish in greater numbers. No-take zones in a Mexican national marine park that had previously been over fished became what they called “large-fish factories.” According to one report, “after 10 years, the area filled back up with big fish – 1,070 percent more fish.” As Dirk Rosen said on our trip, “We want places here where these BOFFs, Big Old Fat Females, can grow big and breed more.” \u003c/p>\n\u003cp>The Donna Kathleen neared its first survey spot and the energy picked up as the crew readied the ROV, named \u003ca href=\"http://www.mnn.com/local-reports/california/nature-conservancy/new-underwater-robot-named-beagle-in-honor-of-darwin%E2%80%99s\">“Beagle,”\u003c/a> for launch. As the boat came to a stop and tilt-a-whirl pitched in the rolling swell, QUEST Associate Producer Josh Cassidy, Audio Tech Eric Limcaoco and I each turned a shade of sea-green and quietly moved to the gunwales to “feed the fish.” We’d basically be out of commission for the rest of the voyage. Thankfully our iron-gutted cameraman, Blake McHugh was able to go on business as usual so were able to capture all the goings-on as the ROV was manhandled and dropped into the deep blue. In a short time it would begin sending amazing images of life on the sea floor back to the scientists watching on board.\u003c/p>\n\u003cp>This is an unusual crew, a blend of rough handed fishermen and conservation biologists working together. The object is to get a \u003ca href=\"http://montereybay.noaa.gov/research/\">baseline \u003c/a>of what is currently living in the MPAs and surrounding areas. In a couple years, and moving forward, scientists can return and survey the same areas to see how, or if, the MPAs are working. \u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>But this \u003ca href=\"http://montereybay.noaa.gov/resourcepro/resmanissues/lostgear.html\">partnership\u003c/a> of fishermen and scientists is something worth noting. These are two groups that have often been at odds during the establishment of the MPAs. But for fisherman Tim Maricich, temporarily converting his fishing boat into a research vessel now made sense. “So research-fishing, fishing-research, in our minds it’s the same. We treat the Beagle like we would a piece of fishing gear. It’s like a large crab trap... If the crab trap was maneuverable and had cameras.” The scientists have been able to access the fisherman's decades-long experience in these waters. And Captain Maricich has been able to have direct input on where data is collected and oversee the operation. “It’s very important for the fishing public to see that this kind of research is being done honestly. It’s imperative to build trust, you know?”\u003c/p>\n\u003cp>This partnership is reflective in another taking place now further North in Ft. Bragg. \u003ca href=\"http://www.opc.ca.gov/2010/05/central-coast-groundfish-project/\">The Central Groundfish Project \u003c/a>is bringing conservationists and fisherman together to develop a new pooled quota system to improve fishery sustainability. The hope is to keep fishermen working while not over fishing. \u003ca href=\"http://www.nature.org/ourinitiatives/regions/northamerica/unitedstates/california/\">The Nature Conservancy \u003c/a>has been working with The Fort Bragg Groundfish Association and the Central Coast Sustainable Groundfish Association to provide scientific data and create a community-focused fishing agreement – called a risk pool – that takes a cooperative approach between local fishery stakeholders to help protect our marine resources. \u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Nearly every fisherman will tell you the same thing; they want strong vibrant fisheries and a healthy environment. They will tell you they want to pass it on to the next generation and none of them want to contribute to a collapse. While there might be arguments about how to fix certain problems, or even if they need to be fixed, the new partnerships and the trust being established now may lead to better understanding. Some changes seem to be inevitable- whether it is less independence or the loss of a favorite fishing spot- but one thing probably wont ever change – and that’s the view I always have when leaning over the side.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>I hesitatingly looked at the weather report the night before. I knew we might be in for it. No rain was forecast but the swell looked bigger than I hoped. So as the sun was rising over Pillar Point Harbor in Half Moon Bay, it was some trepidation that I sighed and boarded the fishing vessel Donna Kathleen. Morning coffees were passed out to those who wanted them and we cast off. As the plucky ship made its way beyond the break, I met with captain \u003ca href=\"http://artliveshere.org/profiles/tim_maricich_bio.html\">Tim Maricich\u003c/a>, the crew, and the two scientists we’d be profiling; Dirk Rosen from \u003ca href=\"http://www.maregroup.org/\">Marine Applied Research and Exploration\u003c/a>, the non-profit who builds and pilots the underwater remotely operated vehicles used to survey the sea floor, and Professor \u003ca href=\"http://sep.csumb.edu/staff/james/\">James Lindholm\u003c/a>, from the \u003ca href=\"http://sep.csumb.edu/ifame/index.php\">Institute of Applied Marine Ecology\u003c/a> at California State University Monterey Bay, who is in charge of chronicling and interpreting everything the ROV encounters. Their collective mission was to survey areas of the newly established Marine Protected Areas approximately 2 miles off the North-Central California coast.\u003c/p>\n\u003cp>\u003ca href=\"http://www.dfg.ca.gov/mlpa/\">Marine Protected Areas\u003c/a>, or “MPAs,” have recently been set aside up and down the coast of California. These are essentially restricted no-fishing zones that have been established to allow fish to breed and grow big with the idea that they will be able replenish State waters. This is different from the standard fishery management practices of the past in that it is aimed to protect entire ecosystems all of the time instead of managing one type of fish at certain times of the year.\u003c/p>\n\u003cp>The science seems to back up the theory. In other parts of the world, marine protected areas have shown success in fish populations growing in both number and size. In one case in Mexico, this type of program has been scientifically proven to be successful in bringing back big fish in greater numbers. No-take zones in a Mexican national marine park that had previously been over fished became what they called “large-fish factories.” According to one report, “after 10 years, the area filled back up with big fish – 1,070 percent more fish.” As Dirk Rosen said on our trip, “We want places here where these BOFFs, Big Old Fat Females, can grow big and breed more.” \u003c/p>\n\u003cp>The Donna Kathleen neared its first survey spot and the energy picked up as the crew readied the ROV, named \u003ca href=\"http://www.mnn.com/local-reports/california/nature-conservancy/new-underwater-robot-named-beagle-in-honor-of-darwin%E2%80%99s\">“Beagle,”\u003c/a> for launch. As the boat came to a stop and tilt-a-whirl pitched in the rolling swell, QUEST Associate Producer Josh Cassidy, Audio Tech Eric Limcaoco and I each turned a shade of sea-green and quietly moved to the gunwales to “feed the fish.” We’d basically be out of commission for the rest of the voyage. Thankfully our iron-gutted cameraman, Blake McHugh was able to go on business as usual so were able to capture all the goings-on as the ROV was manhandled and dropped into the deep blue. In a short time it would begin sending amazing images of life on the sea floor back to the scientists watching on board.\u003c/p>\n\u003cp>This is an unusual crew, a blend of rough handed fishermen and conservation biologists working together. The object is to get a \u003ca href=\"http://montereybay.noaa.gov/research/\">baseline \u003c/a>of what is currently living in the MPAs and surrounding areas. In a couple years, and moving forward, scientists can return and survey the same areas to see how, or if, the MPAs are working. \u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>But this \u003ca href=\"http://montereybay.noaa.gov/resourcepro/resmanissues/lostgear.html\">partnership\u003c/a> of fishermen and scientists is something worth noting. These are two groups that have often been at odds during the establishment of the MPAs. But for fisherman Tim Maricich, temporarily converting his fishing boat into a research vessel now made sense. “So research-fishing, fishing-research, in our minds it’s the same. We treat the Beagle like we would a piece of fishing gear. It’s like a large crab trap... If the crab trap was maneuverable and had cameras.” The scientists have been able to access the fisherman's decades-long experience in these waters. And Captain Maricich has been able to have direct input on where data is collected and oversee the operation. “It’s very important for the fishing public to see that this kind of research is being done honestly. It’s imperative to build trust, you know?”\u003c/p>\n\u003cp>This partnership is reflective in another taking place now further North in Ft. Bragg. \u003ca href=\"http://www.opc.ca.gov/2010/05/central-coast-groundfish-project/\">The Central Groundfish Project \u003c/a>is bringing conservationists and fisherman together to develop a new pooled quota system to improve fishery sustainability. The hope is to keep fishermen working while not over fishing. \u003ca href=\"http://www.nature.org/ourinitiatives/regions/northamerica/unitedstates/california/\">The Nature Conservancy \u003c/a>has been working with The Fort Bragg Groundfish Association and the Central Coast Sustainable Groundfish Association to provide scientific data and create a community-focused fishing agreement – called a risk pool – that takes a cooperative approach between local fishery stakeholders to help protect our marine resources. \u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Nearly every fisherman will tell you the same thing; they want strong vibrant fisheries and a healthy environment. They will tell you they want to pass it on to the next generation and none of them want to contribute to a collapse. While there might be arguments about how to fix certain problems, or even if they need to be fixed, the new partnerships and the trust being established now may lead to better understanding. Some changes seem to be inevitable- whether it is less independence or the loss of a favorite fishing spot- but one thing probably wont ever change – and that’s the view I always have when leaning over the side.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cfigure id=\"attachment_24762\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2011/09/26/the-open-science-movement/foldit/\" rel=\"attachment wp-att-24762\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/FoldIt.jpg\" alt=\"\" title=\"FoldIt\" width=\"640\" height=\"368\" class=\"size-full wp-image-24762\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/09/FoldIt.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/FoldIt-400x230.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Citizen scientists solved the structure of a viral protein that had been stumping scientists for a decade using the video game Foldit.\u003c/figcaption>\u003c/figure>\n\u003cp>As I have talked about previously, science is a \u003ca href=\"http://ww2.kqed.org/quest/2011/03/14/secretive-openness/\">pretty closed system\u003c/a>. Scientists do all the work pretty much in secrecy until they are ready to present a polished story. They then present their results to each other in a language only they can understand. Everyone else then has to count on the media to provide updates on what scientists have discovered. \u003c/p>\n\u003cp>Now don’t get me wrong, the system works very well. It \u003ca href=\"http://www.economist.com/node/21528593?fsrc=scn/fb/wl/ar/anarrayoferrors\">isn’t perfect\u003c/a> especially as results are based on more complex data but it is self correcting and important discoveries are made all the time. But would it be even better if we opened things up a bit?\u003c/p>\n\u003cp>A recent \u003ca href=\"http://the-scientist.com/2011/09/18/public-solves-protein-structure/\">story \u003c/a>about how gamers solved a scientific riddle that had eluded scientists for ten years suggests that more transparent science might be better science. And this is the goal of the Open Science movement.\u003c/p>\n\u003cp>I had the opportunity to interview Joseph Jackson about this open science movement and about his upcoming conference, the Open Science Summit. Joseph is a philosopher, entrepreneur, and activist in the Open Science movement. He is the founder of the \u003ca href=\"http://opensciencesummit.com/\">Open Science Summit\u003c/a>, which occurs for the second time on October 22-23, 2011 in Mountain View and co-founder of \u003ca href=\"http://biocurious.org/\">BioCurious\u003c/a>, the Bay Area biology lab for citizen scientists. \u003c/p>\n\u003cp>Below is an email interview I did with him where I ask about his upcoming summit, what the open science movement hopes to achieve and how someone can get involved if they are interested. Enjoy!\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>What is the Open Science Summit?\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_24767\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/JosephJackson.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/JosephJackson.jpg\" alt=\"Joseph Jackson\" title=\"Joseph Jackson at his lab in Menlo Park, CA. May 17, 2011\" width=\"300\" height=\"200\" class=\"size-full wp-image-24767\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Joseph Jackson at his lab in Menlo Park, CA. May 17, 2011\u003c/figcaption>\u003c/figure>\n\u003cp>The \u003ca href=\"http://opensciencesummit.com/\">Open Science Summit\u003c/a> gathers a broad coalition of individuals and organizations striving to transform our science and innovation system to be radically more effective. We examine the biggest opportunities for distributed collaboration and problem solving, while considering the barriers and obstacles standing in the way of the transition to a more fully Open Science paradigm. This year's Summit covers many topics including the future of scientific publishing and peer review (Open Access), data sharing and the future of data driven science, the effects of the patent system on innovation, personal genomics, collaborative (Open Source) models for drug discovery, and new transparent models for clinical trials. \u003c/p>\n\u003cp>\u003cstrong>What is the Open Science movement trying to achieve that the current scientific system can't?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>By definition, to function, science is supposed to be Open. Indeed, science is arguably humanity's greatest achievement, our most successful, Open Process, for discovering the truths about our universe and then harnessing that knowledge for the benefit of all mankind. In contrast to other human processes (politics, which is an intrinsically contentious undertaking focused on controlling and distributing scarce resources), Science is supposed to be an objective, essentially collaborative endeavor, in which, even when competing, all participants are building on the efforts of one another to improve our collective understanding of reality. In practice, of course science has always been subject to manipulations, government or corporate agendas, distortions, human biases, and other messy realities. \u003c/em>\u003c/p>\n\u003cp>Since the 1980's a series of extremely troubling trends have converged to threaten the very foundations of science and innovation at precisely the time when we need to harness the power of distributed collaboration to solve global problems. There has been an unprecedented explosion of patenting (and the advent of patents for software and biological materials and processes that were never considered patentable subject matter). There has been an erosion of public trust in science, and the institutions of science are under increasing strain (be they government funding agencies like the NIH whose budgets are shrinking, or major research universities which appear increasingly schizophrenic as they struggle to reconcile their ostensible public benefit missions with intense pressure to commercialize technologies developed largely with public funds). \u003c/p>\n\u003cp>We have the chance to adopt new models and build new institutions better suited to conducting distributed, massively data driven, collaborative science in the 21st century. This means we have to change the incentive structures and reputation systems that govern science; moving away from old metrics like impact factor (which has a near death grip on scientist's career prospects) and toward new ways of measuring reputation that reward participation in other kinds of scientific activity that are new of critical importance (commenting on articles after publication,scientific blogging and communication to the public, data curation, and more). \u003c/p>\n\u003cp>\u003cstrong>Do you see Open Science replacing the current system or complementing it?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>In the long run, Open Science will transform the way science is done, enhancing the best aspects of science, while helping correct potential abuses and distortions. There are many interrelated components of Open Science, and I don't expect everyone to embrace every part of the vision. Rather, there is a continuum of openness and we're exploring how to improve each dimension of our innovation system by increasing collaboration where and when we can. Quite often, people seize on one aspect or particular argument about Open Science and may have a defensive reaction. They may have a very strongly held or even instinctive position about the role of the patent system or the sanctity of peer review and protest that \"X\" reform will never work because of \"Y and Z\" when in fact, all of these components are evolving together: Open Science isn't naively proposing that we abolish a particular institution while holding everything else constant...of course this won't happen overnight. \u003c/em>\u003c/p>\n\u003cp>There is immense inertia surrounding the way science is conducted, measured, and rewarded. Many understand that it is time to embrace change; let's just hope that we don't reprove Max Planck's dictum once again in this context: \"Science advances one funeral at a time.\"\u003c/p>\n\u003cp>\u003cstrong>What do you see as the dangers of having people able to do biological experiments in their garage? The benefits?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>The idea of garage biology has received tremendous media attention in recent years, as journalists conjure overhyped images both positive and negative ( garage hobbyist as economic savior creating the next billion dollar enterprise or curing cancer vs. the crazed \"biohacker\" terrorist unleashing a pandemic). \u003c/em>\u003c/p>\n\u003cp>The reality is that we are experiencing a profound shift in humanity's relationship to technology of all kinds, and biotechnology is no exception. Tremendous economic benefits are unlocked when technologies become accessible to a wide pool of innovators and users who can develop new applications with them and ultimately build new products and services. \u003c/p>\n\u003cp>Freedom of scientific inquiry is vital to our society and economy. As terrifying as the thought of garage biology gone wrong is, it is unlikely that regulation is the solution to this concern. Instead, restricting the ability of responsible individuals and groups of independent citizen scientists to conduct research, will not make us safer; though it will make us poorer, both intellectually and materially. \u003c/p>\n\u003cp>\u003cstrong>How can your organization help people do science on their own if they are interested?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>We're holding a \u003ca href=\"http://biocurious.org/classes/\">series of classes\u003c/a> to introduce the public to the fundamentals of modern biotechnology. Certain activities are best done in a group setting, especially when you are first starting out. We're also able to take care of proper disposal of any waste that may be generated. \u003c/em>\u003c/p>\n\u003cp>\u003cstrong>Biological experiments are expensive. What resources are available for people who want to do this on the cheap?\u003c/strong>\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003cem>Of course, I'll say the best way is for you to come on down to \u003ca href=\"http://biocurious.org/\">BioCurious\u003c/a> in Sunnyvale, where we have everything you need to get started. Additionally, there are a number of great science education companies that sell kits that can help you get started. In San Jose, for example is \u003ca href=\"http://www.scienceshopusa.com/\">The Science Shop\u003c/a>. \u003ca href=\"http://www.carolina.com/\">Carolina Biology\u003c/a> is one of the oldest education companies in the US and more recently, one of our own BioCurious team has launched \u003ca href=\"http://cofactorbio.com/\">cofactor bio\u003c/a>, a store aimed at the hobbyist biologist.\u003c/em>\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_24762\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2011/09/26/the-open-science-movement/foldit/\" rel=\"attachment wp-att-24762\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/FoldIt.jpg\" alt=\"\" title=\"FoldIt\" width=\"640\" height=\"368\" class=\"size-full wp-image-24762\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/09/FoldIt.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/FoldIt-400x230.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Citizen scientists solved the structure of a viral protein that had been stumping scientists for a decade using the video game Foldit.\u003c/figcaption>\u003c/figure>\n\u003cp>As I have talked about previously, science is a \u003ca href=\"http://ww2.kqed.org/quest/2011/03/14/secretive-openness/\">pretty closed system\u003c/a>. Scientists do all the work pretty much in secrecy until they are ready to present a polished story. They then present their results to each other in a language only they can understand. Everyone else then has to count on the media to provide updates on what scientists have discovered. \u003c/p>\n\u003cp>Now don’t get me wrong, the system works very well. It \u003ca href=\"http://www.economist.com/node/21528593?fsrc=scn/fb/wl/ar/anarrayoferrors\">isn’t perfect\u003c/a> especially as results are based on more complex data but it is self correcting and important discoveries are made all the time. But would it be even better if we opened things up a bit?\u003c/p>\n\u003cp>A recent \u003ca href=\"http://the-scientist.com/2011/09/18/public-solves-protein-structure/\">story \u003c/a>about how gamers solved a scientific riddle that had eluded scientists for ten years suggests that more transparent science might be better science. And this is the goal of the Open Science movement.\u003c/p>\n\u003cp>I had the opportunity to interview Joseph Jackson about this open science movement and about his upcoming conference, the Open Science Summit. Joseph is a philosopher, entrepreneur, and activist in the Open Science movement. He is the founder of the \u003ca href=\"http://opensciencesummit.com/\">Open Science Summit\u003c/a>, which occurs for the second time on October 22-23, 2011 in Mountain View and co-founder of \u003ca href=\"http://biocurious.org/\">BioCurious\u003c/a>, the Bay Area biology lab for citizen scientists. \u003c/p>\n\u003cp>Below is an email interview I did with him where I ask about his upcoming summit, what the open science movement hopes to achieve and how someone can get involved if they are interested. Enjoy!\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>What is the Open Science Summit?\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_24767\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/JosephJackson.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/JosephJackson.jpg\" alt=\"Joseph Jackson\" title=\"Joseph Jackson at his lab in Menlo Park, CA. May 17, 2011\" width=\"300\" height=\"200\" class=\"size-full wp-image-24767\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Joseph Jackson at his lab in Menlo Park, CA. May 17, 2011\u003c/figcaption>\u003c/figure>\n\u003cp>The \u003ca href=\"http://opensciencesummit.com/\">Open Science Summit\u003c/a> gathers a broad coalition of individuals and organizations striving to transform our science and innovation system to be radically more effective. We examine the biggest opportunities for distributed collaboration and problem solving, while considering the barriers and obstacles standing in the way of the transition to a more fully Open Science paradigm. This year's Summit covers many topics including the future of scientific publishing and peer review (Open Access), data sharing and the future of data driven science, the effects of the patent system on innovation, personal genomics, collaborative (Open Source) models for drug discovery, and new transparent models for clinical trials. \u003c/p>\n\u003cp>\u003cstrong>What is the Open Science movement trying to achieve that the current scientific system can't?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>By definition, to function, science is supposed to be Open. Indeed, science is arguably humanity's greatest achievement, our most successful, Open Process, for discovering the truths about our universe and then harnessing that knowledge for the benefit of all mankind. In contrast to other human processes (politics, which is an intrinsically contentious undertaking focused on controlling and distributing scarce resources), Science is supposed to be an objective, essentially collaborative endeavor, in which, even when competing, all participants are building on the efforts of one another to improve our collective understanding of reality. In practice, of course science has always been subject to manipulations, government or corporate agendas, distortions, human biases, and other messy realities. \u003c/em>\u003c/p>\n\u003cp>Since the 1980's a series of extremely troubling trends have converged to threaten the very foundations of science and innovation at precisely the time when we need to harness the power of distributed collaboration to solve global problems. There has been an unprecedented explosion of patenting (and the advent of patents for software and biological materials and processes that were never considered patentable subject matter). There has been an erosion of public trust in science, and the institutions of science are under increasing strain (be they government funding agencies like the NIH whose budgets are shrinking, or major research universities which appear increasingly schizophrenic as they struggle to reconcile their ostensible public benefit missions with intense pressure to commercialize technologies developed largely with public funds). \u003c/p>\n\u003cp>We have the chance to adopt new models and build new institutions better suited to conducting distributed, massively data driven, collaborative science in the 21st century. This means we have to change the incentive structures and reputation systems that govern science; moving away from old metrics like impact factor (which has a near death grip on scientist's career prospects) and toward new ways of measuring reputation that reward participation in other kinds of scientific activity that are new of critical importance (commenting on articles after publication,scientific blogging and communication to the public, data curation, and more). \u003c/p>\n\u003cp>\u003cstrong>Do you see Open Science replacing the current system or complementing it?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>In the long run, Open Science will transform the way science is done, enhancing the best aspects of science, while helping correct potential abuses and distortions. There are many interrelated components of Open Science, and I don't expect everyone to embrace every part of the vision. Rather, there is a continuum of openness and we're exploring how to improve each dimension of our innovation system by increasing collaboration where and when we can. Quite often, people seize on one aspect or particular argument about Open Science and may have a defensive reaction. They may have a very strongly held or even instinctive position about the role of the patent system or the sanctity of peer review and protest that \"X\" reform will never work because of \"Y and Z\" when in fact, all of these components are evolving together: Open Science isn't naively proposing that we abolish a particular institution while holding everything else constant...of course this won't happen overnight. \u003c/em>\u003c/p>\n\u003cp>There is immense inertia surrounding the way science is conducted, measured, and rewarded. Many understand that it is time to embrace change; let's just hope that we don't reprove Max Planck's dictum once again in this context: \"Science advances one funeral at a time.\"\u003c/p>\n\u003cp>\u003cstrong>What do you see as the dangers of having people able to do biological experiments in their garage? The benefits?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>The idea of garage biology has received tremendous media attention in recent years, as journalists conjure overhyped images both positive and negative ( garage hobbyist as economic savior creating the next billion dollar enterprise or curing cancer vs. the crazed \"biohacker\" terrorist unleashing a pandemic). \u003c/em>\u003c/p>\n\u003cp>The reality is that we are experiencing a profound shift in humanity's relationship to technology of all kinds, and biotechnology is no exception. Tremendous economic benefits are unlocked when technologies become accessible to a wide pool of innovators and users who can develop new applications with them and ultimately build new products and services. \u003c/p>\n\u003cp>Freedom of scientific inquiry is vital to our society and economy. As terrifying as the thought of garage biology gone wrong is, it is unlikely that regulation is the solution to this concern. Instead, restricting the ability of responsible individuals and groups of independent citizen scientists to conduct research, will not make us safer; though it will make us poorer, both intellectually and materially. \u003c/p>\n\u003cp>\u003cstrong>How can your organization help people do science on their own if they are interested?\u003c/strong>\u003c/p>\n\u003cp>\u003cem>We're holding a \u003ca href=\"http://biocurious.org/classes/\">series of classes\u003c/a> to introduce the public to the fundamentals of modern biotechnology. Certain activities are best done in a group setting, especially when you are first starting out. We're also able to take care of proper disposal of any waste that may be generated. \u003c/em>\u003c/p>\n\u003cp>\u003cstrong>Biological experiments are expensive. What resources are available for people who want to do this on the cheap?\u003c/strong>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cem>Of course, I'll say the best way is for you to come on down to \u003ca href=\"http://biocurious.org/\">BioCurious\u003c/a> in Sunnyvale, where we have everything you need to get started. Additionally, there are a number of great science education companies that sell kits that can help you get started. In San Jose, for example is \u003ca href=\"http://www.scienceshopusa.com/\">The Science Shop\u003c/a>. \u003ca href=\"http://www.carolina.com/\">Carolina Biology\u003c/a> is one of the oldest education companies in the US and more recently, one of our own BioCurious team has launched \u003ca href=\"http://cofactorbio.com/\">cofactor bio\u003c/a>, a store aimed at the hobbyist biologist.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>We're excited to present our second \u003cem>Your Videos on QUEST\u003c/em> segment featuring an excerpt of the short video by Dan Griffin of GG Films, \"Ocean Babies on Acid\". For several years now, QUEST has been producing \u003cem>\u003ca href=\"http://ww2.kqed.org/quest/video/your-photos-on-quest-bryant-austin/\">Your Photos on QUEST\u003c/a>\u003c/em> segments wherein we feature the still images of Bay Area photographers who shoot nature, environment and science photos. \u003c/p>\n\u003cp>This season, we wanted to expand that idea to include films and videos on similar topics. The thinking is, we here on QUEST are never at a loss for story topics about science here in the Bay Area. There must be a bunch of other media makers telling these kinds of stories so let's get some different perspectives from the community. \u003c/p>\n\u003cfigure id=\"attachment_24170\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/508i-Palumbi_640-300x169.jpg\" alt=\"\" title=\"508i Palumbi_640\" width=\"300\" height=\"169\" class=\"size-thumbnail wp-image-24170\">\u003cfigcaption class=\"wp-caption-text\">Stanford marine biologist, Stephen Palumbi\u003c/figcaption>\u003c/figure>\n\u003cp>QUEST folks have long been fans of the video work that \u003ca href=\"http://ggfilms.com/\">Dan Griffin/ GG Films\u003c/a> has been doing with Stanford marine biologist, \u003ca href=\"http://palumbi.stanford.edu/\">Stephen Palumbi\u003c/a>. Together they create \u003ca href=\"http://www.stanford.edu/group/microdocs\">\"Microdocs\"\u003c/a> which they define as \"short attention span science video.\" Their videos are usually 2-3 minutes long and feature one specific aspect of marine ecosystem sustainability. Microdocs topics focus largely on coral reef health, sustainability and diversity- subjects that have required them to travel to such remote tropical locations as American Samoa, The Bahamas, Fiji and Micronesia. Ahh, the price that we pay for our art...\u003c/p>\n\u003cfigure id=\"attachment_24165\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/508i-urchin-large-beaker_640-300x169.jpg\" alt=\"\" title=\"508i urchin large beaker_640\" width=\"300\" height=\"169\" class=\"size-thumbnail wp-image-24165\">\u003cfigcaption class=\"wp-caption-text\">Purple sea urchin in beaker\u003c/figcaption>\u003c/figure>\n\u003cp>\"Ocean Babies on Acid\" focuses on an experiment that Stephen Palumbi and UC Davis marine biologist \u003ca href=\"http://bml.ucdavis.edu/research/faculty/eric-sanford/\">Eric Sanford\u003c/a> are doing to study the effects of \u003ca href=\"http://ww2.kqed.org/quest/video/acidic-seas/\">ocean acidification\u003c/a> on sea urchin larvae off the California and Oregon coasts. One of their goals is to find out if the increased acidity caused in part by increased CO2 levels in the atmosphere makes it difficult for marine species to grow their shells. The study is unique in that they're not only studying the external aspects of these creatures but also delving into how ocean acidification may effect the animals on a genetic level. \u003c/p>\n\u003cp>You can watch the full-length video on the Microdocs site here:\u003cbr>\n\u003ca href=\"http://www.stanford.edu/group/microdocs/index.html\">Ocean Babies on Acid\u003c/a>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\u003cp>\u003c/p>\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>We're excited to present our second \u003cem>Your Videos on QUEST\u003c/em> segment featuring an excerpt of the short video by Dan Griffin of GG Films, \"Ocean Babies on Acid\". For several years now, QUEST has been producing \u003cem>\u003ca href=\"http://ww2.kqed.org/quest/video/your-photos-on-quest-bryant-austin/\">Your Photos on QUEST\u003c/a>\u003c/em> segments wherein we feature the still images of Bay Area photographers who shoot nature, environment and science photos. \u003c/p>\n\u003cp>This season, we wanted to expand that idea to include films and videos on similar topics. The thinking is, we here on QUEST are never at a loss for story topics about science here in the Bay Area. There must be a bunch of other media makers telling these kinds of stories so let's get some different perspectives from the community. \u003c/p>\n\u003cfigure id=\"attachment_24170\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/508i-Palumbi_640-300x169.jpg\" alt=\"\" title=\"508i Palumbi_640\" width=\"300\" height=\"169\" class=\"size-thumbnail wp-image-24170\">\u003cfigcaption class=\"wp-caption-text\">Stanford marine biologist, Stephen Palumbi\u003c/figcaption>\u003c/figure>\n\u003cp>QUEST folks have long been fans of the video work that \u003ca href=\"http://ggfilms.com/\">Dan Griffin/ GG Films\u003c/a> has been doing with Stanford marine biologist, \u003ca href=\"http://palumbi.stanford.edu/\">Stephen Palumbi\u003c/a>. Together they create \u003ca href=\"http://www.stanford.edu/group/microdocs\">\"Microdocs\"\u003c/a> which they define as \"short attention span science video.\" Their videos are usually 2-3 minutes long and feature one specific aspect of marine ecosystem sustainability. Microdocs topics focus largely on coral reef health, sustainability and diversity- subjects that have required them to travel to such remote tropical locations as American Samoa, The Bahamas, Fiji and Micronesia. Ahh, the price that we pay for our art...\u003c/p>\n\u003cfigure id=\"attachment_24165\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/508i-urchin-large-beaker_640-300x169.jpg\" alt=\"\" title=\"508i urchin large beaker_640\" width=\"300\" height=\"169\" class=\"size-thumbnail wp-image-24165\">\u003cfigcaption class=\"wp-caption-text\">Purple sea urchin in beaker\u003c/figcaption>\u003c/figure>\n\u003cp>\"Ocean Babies on Acid\" focuses on an experiment that Stephen Palumbi and UC Davis marine biologist \u003ca href=\"http://bml.ucdavis.edu/research/faculty/eric-sanford/\">Eric Sanford\u003c/a> are doing to study the effects of \u003ca href=\"http://ww2.kqed.org/quest/video/acidic-seas/\">ocean acidification\u003c/a> on sea urchin larvae off the California and Oregon coasts. One of their goals is to find out if the increased acidity caused in part by increased CO2 levels in the atmosphere makes it difficult for marine species to grow their shells. The study is unique in that they're not only studying the external aspects of these creatures but also delving into how ocean acidification may effect the animals on a genetic level. \u003c/p>\n\u003cp>You can watch the full-length video on the Microdocs site here:\u003cbr>\n\u003ca href=\"http://www.stanford.edu/group/microdocs/index.html\">Ocean Babies on Acid\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cp>It is high season for tomatoes right now. Your local farmers’ market probably has a whole color spectrum of heirloom tomatoes, from red to green and purple, deepening to almost black. Heirloom tomatoes are getting more and more popular—but what does “heirloom” really mean? And how do these colorful tomatoes differ from their supermarket relatives?\u003c/p>\n\u003cp>\u003cstrong>What does “heirloom” mean, anyway?\u003c/strong>\u003cbr>\nIn agriculture, the word “heirloom” doesn’t have a precise definition. It conjures up ideas of a food that is old fashioned and has been handed down for generations—which is as good a definition as any right now. Heirloom tomatoes are varieties that have been grown without crossbreeding for 40 or more years. This is in contrast to the typical supermarket tomatoes, which are \u003ca href=\"http://en.wikipedia.org/wiki/Hybrid_%28biology%29\">hybrids\u003c/a> that have been carefully crossbred to have particular characteristics. Often flavor is not at the top of the list. Instead, hybrid tomatoes are bred for things like resistance to pests and diseases, and firm flesh and thick skin—so they can be harvested by machines and emerge as whole tomatoes, not sauce.\u003c/p>\n\u003cp>But genetic mixing—or lack thereof—isn’t the only thing that separates the heirlooms and the hybrids. Let’s look at some heirloom tomato myths and truths, to get at other difference between the two tomatoes.\u003c/p>\n\u003cp>\u003cstrong>You can grow heirloom tomatoes from their seeds.\u003c/strong>\u003cbr>\nCorrect. \u003cdel datetime=\"2011-09-13T06:42:22+00:00\">Hybrid\u003c/del> Heirloom tomatoes breed true—if you take the seeds from your heirloom tomatoes, treat them right, and then plant them in the spring, the tomatoes you pluck from the vines in late summer will taste just like their parents tasted. One characteristic of heirloom crops is that they are \u003ca href=\"http://en.wikipedia.org/wiki/Open_pollination\">open-pollinated\u003c/a>; pollen is carried by natural mechanisms, like bees or wind. Compare this to commercially grown hybrid tomatoes, which must be pollinated by hand to ensure the correct combination of traits. This is a lot of work, but it’s necessary. Open-pollinated hybrid seeds might carry the good genes for a particular trait, or they might the carry bad genes. The only way to ensure a good crop of hybrids is to plant seeds that have been hand-pollinated so you get the right mix.\u003c/p>\n\u003cp>\u003cstrong>Heirloom tomatoes are organic.\u003c/strong>\u003cbr>\nNot necessarily. Often they are organic, but they would still be called heirlooms if growers treated them with pesticides and other chemicals. And growers would have good reason to spray: heirlooms don’t have the disease and pest resistance that hybrids have acquired over generations of selective breeding. Heirlooms are particularly susceptible to fungus, which makes them crack and split. Farmers growing heirlooms get one-third the yield (or even less) than they would if they were growing hybrids, because so many plants and fruits are damaged by pests and disease. This is one reason why heirloom tomatoes are so expensive.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>Heirlooms taste better.\u003c/strong>\u003cbr>\nOften this is true, and there are a couple of reasons for it; some are inherent to heirlooms, and some are byproducts of the way they’re grown and harvested. An heirloom tomato plant often produces a total of only two fruits; all the plant’s reproductive efforts get concentrated into just a few tomatoes. This concentrated effort could be making the tomatoes more flavorful. And, heirlooms usually have more locules—the cavities with the seeds—than commercial hybrids. These locules are flavor centers, full of volatile compounds. Hybrids are less flavorful because they were never bred for flavor—although \u003ca href=\"http://www.smithsonianmag.com/science-nature/passion-for-tomatoes.html\">that is changing\u003c/a>. Plus, heirlooms are often grown locally and allowed to ripen on the vine, as opposed to typical supermarket hybrids, which are picked when firm and green, and are ripened to redness in a warehouse with ethylene gas. When and how tomatoes ripen affects their flavor.\u003c/p>\n\u003cp>\u003cstrong>Heirlooms are better for you.\u003c/strong>\u003cbr>\nFalse: there is no evidence for this. Heirlooms don’t have more nutrients or anti-oxidants than hybrids.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cstrong>A tomato tip.\u003c/strong>\u003cbr>\nWhether your shopping cart is full of heirlooms or hybrids, whether they’re red or yellow or deep purple, don’t put those tomatoes in the fridge. The cold temperature decreases whatever flavor they may have.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>It is high season for tomatoes right now. Your local farmers’ market probably has a whole color spectrum of heirloom tomatoes, from red to green and purple, deepening to almost black. Heirloom tomatoes are getting more and more popular—but what does “heirloom” really mean? And how do these colorful tomatoes differ from their supermarket relatives?\u003c/p>\n\u003cp>\u003cstrong>What does “heirloom” mean, anyway?\u003c/strong>\u003cbr>\nIn agriculture, the word “heirloom” doesn’t have a precise definition. It conjures up ideas of a food that is old fashioned and has been handed down for generations—which is as good a definition as any right now. Heirloom tomatoes are varieties that have been grown without crossbreeding for 40 or more years. This is in contrast to the typical supermarket tomatoes, which are \u003ca href=\"http://en.wikipedia.org/wiki/Hybrid_%28biology%29\">hybrids\u003c/a> that have been carefully crossbred to have particular characteristics. Often flavor is not at the top of the list. Instead, hybrid tomatoes are bred for things like resistance to pests and diseases, and firm flesh and thick skin—so they can be harvested by machines and emerge as whole tomatoes, not sauce.\u003c/p>\n\u003cp>But genetic mixing—or lack thereof—isn’t the only thing that separates the heirlooms and the hybrids. Let’s look at some heirloom tomato myths and truths, to get at other difference between the two tomatoes.\u003c/p>\n\u003cp>\u003cstrong>You can grow heirloom tomatoes from their seeds.\u003c/strong>\u003cbr>\nCorrect. \u003cdel datetime=\"2011-09-13T06:42:22+00:00\">Hybrid\u003c/del> Heirloom tomatoes breed true—if you take the seeds from your heirloom tomatoes, treat them right, and then plant them in the spring, the tomatoes you pluck from the vines in late summer will taste just like their parents tasted. One characteristic of heirloom crops is that they are \u003ca href=\"http://en.wikipedia.org/wiki/Open_pollination\">open-pollinated\u003c/a>; pollen is carried by natural mechanisms, like bees or wind. Compare this to commercially grown hybrid tomatoes, which must be pollinated by hand to ensure the correct combination of traits. This is a lot of work, but it’s necessary. Open-pollinated hybrid seeds might carry the good genes for a particular trait, or they might the carry bad genes. The only way to ensure a good crop of hybrids is to plant seeds that have been hand-pollinated so you get the right mix.\u003c/p>\n\u003cp>\u003cstrong>Heirloom tomatoes are organic.\u003c/strong>\u003cbr>\nNot necessarily. Often they are organic, but they would still be called heirlooms if growers treated them with pesticides and other chemicals. And growers would have good reason to spray: heirlooms don’t have the disease and pest resistance that hybrids have acquired over generations of selective breeding. Heirlooms are particularly susceptible to fungus, which makes them crack and split. Farmers growing heirlooms get one-third the yield (or even less) than they would if they were growing hybrids, because so many plants and fruits are damaged by pests and disease. This is one reason why heirloom tomatoes are so expensive.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>Heirlooms taste better.\u003c/strong>\u003cbr>\nOften this is true, and there are a couple of reasons for it; some are inherent to heirlooms, and some are byproducts of the way they’re grown and harvested. An heirloom tomato plant often produces a total of only two fruits; all the plant’s reproductive efforts get concentrated into just a few tomatoes. This concentrated effort could be making the tomatoes more flavorful. And, heirlooms usually have more locules—the cavities with the seeds—than commercial hybrids. These locules are flavor centers, full of volatile compounds. Hybrids are less flavorful because they were never bred for flavor—although \u003ca href=\"http://www.smithsonianmag.com/science-nature/passion-for-tomatoes.html\">that is changing\u003c/a>. Plus, heirlooms are often grown locally and allowed to ripen on the vine, as opposed to typical supermarket hybrids, which are picked when firm and green, and are ripened to redness in a warehouse with ethylene gas. When and how tomatoes ripen affects their flavor.\u003c/p>\n\u003cp>\u003cstrong>Heirlooms are better for you.\u003c/strong>\u003cbr>\nFalse: there is no evidence for this. Heirlooms don’t have more nutrients or anti-oxidants than hybrids.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cstrong>A tomato tip.\u003c/strong>\u003cbr>\nWhether your shopping cart is full of heirlooms or hybrids, whether they’re red or yellow or deep purple, don’t put those tomatoes in the fridge. The cold temperature decreases whatever flavor they may have.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Turning Chickens into Dinosaurs",
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"content": "\u003cfigure id=\"attachment_24035\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/dinochicken3.jpg\">\u003cimg class=\"size-thumbnail wp-image-24035\" title=\"dinochicken3\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/dinochicken3-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.\u003c/figcaption>\u003c/figure>\n\u003cp>You may remember that in Jurassic Park, scientists sequenced some dinosaur DNA from a mosquito trapped in amber. They made a copy of this DNA, filled in the gaps with frog DNA and then created a dinosaur.\u003c/p>\n\u003cp>Although cool, we're not likely to get dinosaurs this way in the near future for a bunch of different reasons. The biggest for now (besides not having any dinosaur DNA) is that we can’t \u003ca href=\"http://www.thetech.org/genetics/news.php?id=129\">clone anything bigger than a bacterium\u003c/a> with just a piece of DNA. To clone a multi-celled creature like a dinosaur, we need frozen or even better, live cells.\u003c/p>\n\u003cp>While this might be possible for some extinct animals including \u003ca href=\"http://ww2.kqed.org/quest/2008/11/10/mammoth-resurrection/\">mammoths\u003c/a>, 65 million years is just too long to find any frozen or viable cells. But there may be another way to one day create Jurassic Park. By messing with a chicken’s genes.\u003c/p>\n\u003cp>Current theories are that birds evolved from dinosaurs. This means that all the information for making a dinosaur was contained in bird DNA at one time. The trick is to figure out what this dinosaur DNA looked like and to change bird DNA accordingly and/or to unlock any hidden dinosaur DNA that may still be in bird DNA.\u003c/p>\n\u003cp>After 65 million years you might think all traces of dino-DNA would be lost in birds. Surprisingly, you’d be wrong. It looks like there is still some T-rex lurking in a chicken’s DNA.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>In the last decade, scientists have been able to make chickens look a bit more dinosaur-like by changing how the chickens use the genes they already have. For example, they have been able to make a chicken’s tail look a bit more like a dinosaur’s.\u003c/p>\n\u003cp>A big difference between birds and dinosaurs is that dinosaurs have much longer tails. But this doesn’t hold up in a chicken embryo.\u003c/p>\n\u003cp>At a very early stage of development, chicken embryos have what looks like a very reptilian tail with 16 vertebrae. Later in development, though, most of the vertebrae disappear until only five are left.\u003c/p>\n\u003cp>What this means is that if scientists can figure out how to keep the vertebrae from disappearing, they might end up with a long tailed chicken. And they’ve actually managed to sort of do this already.\u003c/p>\n\u003cp>By changing when certain genes are turned on or off, they have managed to \u003ca href=\"http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html\">create a chicken\u003c/a> with a tail that has eight vertebrae. Not quite a dinosaur but a step in that direction.\u003c/p>\n\u003cp>They have also been able to create a \u003ca href=\"http://dml.cmnh.org/2011Aug/msg00313.html\">chicken with teeth\u003c/a>. And even a \u003ca href=\"http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html\">snout\u003c/a>! All of this without fundamentally changing a chicken’s genes but instead changing how they are used.\u003c/p>\n\u003cp>Now they probably won’t be able to make the chicken-dinosaur transition simply by changing how chicken genes are used. There are bound to have been some significant changes in certain key genes that will have to be replicated to really make a dinosaur. And for that we’ll need to figure out what dinosaur DNA looked like.\u003c/p>\n\u003cp>But still, we can make a lot of progress towards making a dinosaur by simply using the toolkit of current bird genes. In the end, we’ll probably be able to recreate something very much like a dinosaur. The question will then become whether we should.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>QUEST story on how scientists can figure out ancient DNA from modern DNA.\u003c/em>\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_24035\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/dinochicken3.jpg\">\u003cimg class=\"size-thumbnail wp-image-24035\" title=\"dinochicken3\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/dinochicken3-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">By reversing evolution, scientists may be able to transform chickens into dinosaurs one step at a time.\u003c/figcaption>\u003c/figure>\n\u003cp>You may remember that in Jurassic Park, scientists sequenced some dinosaur DNA from a mosquito trapped in amber. They made a copy of this DNA, filled in the gaps with frog DNA and then created a dinosaur.\u003c/p>\n\u003cp>Although cool, we're not likely to get dinosaurs this way in the near future for a bunch of different reasons. The biggest for now (besides not having any dinosaur DNA) is that we can’t \u003ca href=\"http://www.thetech.org/genetics/news.php?id=129\">clone anything bigger than a bacterium\u003c/a> with just a piece of DNA. To clone a multi-celled creature like a dinosaur, we need frozen or even better, live cells.\u003c/p>\n\u003cp>While this might be possible for some extinct animals including \u003ca href=\"http://ww2.kqed.org/quest/2008/11/10/mammoth-resurrection/\">mammoths\u003c/a>, 65 million years is just too long to find any frozen or viable cells. But there may be another way to one day create Jurassic Park. By messing with a chicken’s genes.\u003c/p>\n\u003cp>Current theories are that birds evolved from dinosaurs. This means that all the information for making a dinosaur was contained in bird DNA at one time. The trick is to figure out what this dinosaur DNA looked like and to change bird DNA accordingly and/or to unlock any hidden dinosaur DNA that may still be in bird DNA.\u003c/p>\n\u003cp>After 65 million years you might think all traces of dino-DNA would be lost in birds. Surprisingly, you’d be wrong. It looks like there is still some T-rex lurking in a chicken’s DNA.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>In the last decade, scientists have been able to make chickens look a bit more dinosaur-like by changing how the chickens use the genes they already have. For example, they have been able to make a chicken’s tail look a bit more like a dinosaur’s.\u003c/p>\n\u003cp>A big difference between birds and dinosaurs is that dinosaurs have much longer tails. But this doesn’t hold up in a chicken embryo.\u003c/p>\n\u003cp>At a very early stage of development, chicken embryos have what looks like a very reptilian tail with 16 vertebrae. Later in development, though, most of the vertebrae disappear until only five are left.\u003c/p>\n\u003cp>What this means is that if scientists can figure out how to keep the vertebrae from disappearing, they might end up with a long tailed chicken. And they’ve actually managed to sort of do this already.\u003c/p>\n\u003cp>By changing when certain genes are turned on or off, they have managed to \u003ca href=\"http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html\">create a chicken\u003c/a> with a tail that has eight vertebrae. Not quite a dinosaur but a step in that direction.\u003c/p>\n\u003cp>They have also been able to create a \u003ca href=\"http://dml.cmnh.org/2011Aug/msg00313.html\">chicken with teeth\u003c/a>. And even a \u003ca href=\"http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html\">snout\u003c/a>! All of this without fundamentally changing a chicken’s genes but instead changing how they are used.\u003c/p>\n\u003cp>Now they probably won’t be able to make the chicken-dinosaur transition simply by changing how chicken genes are used. There are bound to have been some significant changes in certain key genes that will have to be replicated to really make a dinosaur. And for that we’ll need to figure out what dinosaur DNA looked like.\u003c/p>\n\u003cp>But still, we can make a lot of progress towards making a dinosaur by simply using the toolkit of current bird genes. In the end, we’ll probably be able to recreate something very much like a dinosaur. The question will then become whether we should.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>QUEST story on how scientists can figure out ancient DNA from modern DNA.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>While the massive scale of Bryant Austin’s life-sized whale photographs has an instantaneous and undeniable awing effect, it is the sense of emotional connection to his subjects that makes the images stick in the viewer’s mind. These are photographs taken with the cooperation of the whales. Mr. Austin has dedicated his life to creating bonds with wild whales, and his photographs are the records of his interactions with them. Swimming alongside these giants is an experience less than one millionth of 1% of the human population will experience.\u003c/p>\n\u003cfigure id=\"attachment_23480\" class=\"wp-caption alignright\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1440x928.jpg\" alt=\"A whale swims away from Bryant Austin\" width=\"640\" height=\"412\" class=\"size-large wp-image-23480\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1440x928.jpg 1440w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-400x258.jpg 400w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-800x515.jpg 800w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1180x760.jpg 1180w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-960x618.jpg 960w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">A whale swims away from Bryant Austin as he snorkels. \u003ccite>(Bryant Austin)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Before he takes the plunge, Mr. Austin spends months preparing to film in the wild by working with whale biologists who study specific populations of whales. Mr. Austin travels with these experts, to identify unique individual whales who posses the personality and sense of curiosity to be agreeable subjects. Austin returns to the whales day after day to build a sense of familiarity which will eventually allow them to feel comfortable enough to approach him on their own terms. Swimming with whales is intrinsically very dangerous if for no other reason than their enormous size. A single accidental flick from a pectoral fin or fluke could pummel a human swimmer. A threatened whale or a mother protecting her calf can be particularly dangerous. While whales have the potential to be destructive, it is much more likely that a whale disturbed by a human swimmer will simply swim away. For this reason Austin works hard to build the trust of his subjects. \u003c/p>\n\u003cp>Whales, like humans, are intelligent mammals that live within social structures. As such, whales have a kind of etiquette based on behavioral cues. To get close enough to photograph the whales Mr. Austin has to abide by a different species code of conduct. For example, Austin does not use SCUBA while visiting the whales because the bubbles produced by the equipment can be construed as a threat display between whales. \u003c/p>\n\u003cp>“Although we can’t communicate with whales verbally, you can communicate intention. And I do this by being very slow and predictable when I move. And I remain motionless most of the time, and I want to communicate to them that I’m interested in them, but I’m also respectful, and I’m just going be very passive and patient. Most of the time, they ignore me or swim away, and there’s just that, those few exceptional moments in the season where they decide to come up to me and spend a few moments” \u003cbr>It's within these few rare moments that Bryant Austin is able to create his stunning photographs. In fact, his entire collection to date represents interactions with only 9 particularly curious individual whales. As top predators, whales generally tend to demonstrate curiosity in exploring their environment. Some species like humpback whales tend to be more curious than other species, but even within a species individual whales will show different personality traits. Through his non-profit organization \u003ca href=\"http://mmcta.org/\">Marine Mammal Conservation Through the Arts\u003c/a>, Mr. Austin works for months for the brief seconds and minutes when the whales come to inspect him. \u003c/p>\n\u003cp>\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/1k-Bryant-Austin-Minke-Whale-Composite-One-at-the-Tamada-Museum-Tokyo-450x253.jpg\" alt=\"A visitor at Tokyo's Tamada Museum views Bryant Austin's life-sized print of a Minke Whale\" title=\"1k Bryant Austin Minke Whale Composite One at the Tamada Museum Tokyo\" width=\"450\" height=\"253\" class=\"alignright size-medium wp-image-23481\">\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>“The camera I’m holding in a way is like the world’s eye, humanity’s eye, so we can make whales visible and hopefully change our perception and behavior towards them. So it’s ironic that this little 210-pound person really can be more powerful than this 40-ton whale.” \u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>While the massive scale of Bryant Austin’s life-sized whale photographs has an instantaneous and undeniable awing effect, it is the sense of emotional connection to his subjects that makes the images stick in the viewer’s mind. These are photographs taken with the cooperation of the whales. Mr. Austin has dedicated his life to creating bonds with wild whales, and his photographs are the records of his interactions with them. Swimming alongside these giants is an experience less than one millionth of 1% of the human population will experience.\u003c/p>\n\u003cfigure id=\"attachment_23480\" class=\"wp-caption alignright\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1440x928.jpg\" alt=\"A whale swims away from Bryant Austin\" width=\"640\" height=\"412\" class=\"size-large wp-image-23480\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1440x928.jpg 1440w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-400x258.jpg 400w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-800x515.jpg 800w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-1180x760.jpg 1180w, https://ww2.kqed.org/app/uploads/sites/39/2011/09/DominicaBryantAustin8April2011_MG_5927-Image-from-Sylvia-Earl-960x618.jpg 960w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">A whale swims away from Bryant Austin as he snorkels. \u003ccite>(Bryant Austin)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Before he takes the plunge, Mr. Austin spends months preparing to film in the wild by working with whale biologists who study specific populations of whales. Mr. Austin travels with these experts, to identify unique individual whales who posses the personality and sense of curiosity to be agreeable subjects. Austin returns to the whales day after day to build a sense of familiarity which will eventually allow them to feel comfortable enough to approach him on their own terms. Swimming with whales is intrinsically very dangerous if for no other reason than their enormous size. A single accidental flick from a pectoral fin or fluke could pummel a human swimmer. A threatened whale or a mother protecting her calf can be particularly dangerous. While whales have the potential to be destructive, it is much more likely that a whale disturbed by a human swimmer will simply swim away. For this reason Austin works hard to build the trust of his subjects. \u003c/p>\n\u003cp>Whales, like humans, are intelligent mammals that live within social structures. As such, whales have a kind of etiquette based on behavioral cues. To get close enough to photograph the whales Mr. Austin has to abide by a different species code of conduct. For example, Austin does not use SCUBA while visiting the whales because the bubbles produced by the equipment can be construed as a threat display between whales. \u003c/p>\n\u003cp>“Although we can’t communicate with whales verbally, you can communicate intention. And I do this by being very slow and predictable when I move. And I remain motionless most of the time, and I want to communicate to them that I’m interested in them, but I’m also respectful, and I’m just going be very passive and patient. Most of the time, they ignore me or swim away, and there’s just that, those few exceptional moments in the season where they decide to come up to me and spend a few moments” \u003cbr>It's within these few rare moments that Bryant Austin is able to create his stunning photographs. In fact, his entire collection to date represents interactions with only 9 particularly curious individual whales. As top predators, whales generally tend to demonstrate curiosity in exploring their environment. Some species like humpback whales tend to be more curious than other species, but even within a species individual whales will show different personality traits. Through his non-profit organization \u003ca href=\"http://mmcta.org/\">Marine Mammal Conservation Through the Arts\u003c/a>, Mr. Austin works for months for the brief seconds and minutes when the whales come to inspect him. \u003c/p>\n\u003cp>\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/1k-Bryant-Austin-Minke-Whale-Composite-One-at-the-Tamada-Museum-Tokyo-450x253.jpg\" alt=\"A visitor at Tokyo's Tamada Museum views Bryant Austin's life-sized print of a Minke Whale\" title=\"1k Bryant Austin Minke Whale Composite One at the Tamada Museum Tokyo\" width=\"450\" height=\"253\" class=\"alignright size-medium wp-image-23481\">\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cp>Every day, San Francisco’s compostables – all 600 tons of them – are hauled away from the city. I found myself asking, “Where does it all go?”\u003c/p>\n\u003cp>While looking for the answers, I found agronomist Bob Shaffer. Shaffer started out as a farmer, but soon realized that he was more interested in the soil than in what grew out of it. That led to a career in making and applying compost. He now works with \u003ca href=\"http://www.recology.com/index.htm\">Recology\u003c/a>, the company that composts San Francisco's green waste, at their \u003ca href=\"http://www.jepsonprairieorganics.com/\">composting facility in Vacaville\u003c/a> and with farmers who want to improve their crops.\u003c/p>\n\u003cp>One of Shaffer’s clients is \u003ca href=\"http://www.buckzin.com/index.html\">Old Hill Ranch\u003c/a> in Glen Ellen. As the name suggests, the vineyard is one of the earliest in Sonoma County and has many 100-year-old vines.\u003c/p>\n\u003cp>When Old Hill was first established, it was planted in the traditional way – a lot of different grape varietals were planted, producing a blended wine. The vineyard has a colorful map that identifies the patchwork of varietals on the property.\u003c/p>\n\u003cp>The vines are dry farmed, with no irrigation system running between the vine rows. This makes adding compost really important, as it helps with water retention in the soil. Old Hill’s owner, Will Bucklin, is also experimenting with compost tea, in which a small amount of compost is “brewed” into a dark tea to develop beneficial microbes. The tea can be added to a water supply or sprayed onto the leaves directly. It’s another way of making nutrients and protective microbes available to the plant.\u003c/p>\n\u003cfigure id=\"attachment_23733\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/Compost_grapes_640.jpg\">\u003cimg class=\"size-thumbnail wp-image-23733\" title=\"Compost_grapes_640\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/Compost_grapes_640-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Tiny young grapes on a vine at Old Hill Ranch, in Glen Ellen. Photo: Kate Szrom.\u003c/figcaption>\u003c/figure>\n\u003cp>When QUEST visited Old Hill Ranch, it was a hot, sunny June day. There had just been a full moon and the blooms on the vines had set into tiny green grapes.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>As he does in the summer season, Shaffer checked to see if the vines were getting water and nutrients by observing the leaves and tendrils on the vines. He pointed out some of the cover crops he has planted to prevent soil erosion. Through their roots, cover crops like grasses and legumes can also carry carbon deeper into the soil than compost alone would.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>In the fall, compost will be applied at Old Hill and on other vineyards like it. Over the winter, rains will help spread the nutrients and beneficial microbes in the compost through the ground to be made available for next year’s growing season.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>Every day, San Francisco’s compostables – all 600 tons of them – are hauled away from the city. I found myself asking, “Where does it all go?”\u003c/p>\n\u003cp>While looking for the answers, I found agronomist Bob Shaffer. Shaffer started out as a farmer, but soon realized that he was more interested in the soil than in what grew out of it. That led to a career in making and applying compost. He now works with \u003ca href=\"http://www.recology.com/index.htm\">Recology\u003c/a>, the company that composts San Francisco's green waste, at their \u003ca href=\"http://www.jepsonprairieorganics.com/\">composting facility in Vacaville\u003c/a> and with farmers who want to improve their crops.\u003c/p>\n\u003cp>One of Shaffer’s clients is \u003ca href=\"http://www.buckzin.com/index.html\">Old Hill Ranch\u003c/a> in Glen Ellen. As the name suggests, the vineyard is one of the earliest in Sonoma County and has many 100-year-old vines.\u003c/p>\n\u003cp>When Old Hill was first established, it was planted in the traditional way – a lot of different grape varietals were planted, producing a blended wine. The vineyard has a colorful map that identifies the patchwork of varietals on the property.\u003c/p>\n\u003cp>The vines are dry farmed, with no irrigation system running between the vine rows. This makes adding compost really important, as it helps with water retention in the soil. Old Hill’s owner, Will Bucklin, is also experimenting with compost tea, in which a small amount of compost is “brewed” into a dark tea to develop beneficial microbes. The tea can be added to a water supply or sprayed onto the leaves directly. It’s another way of making nutrients and protective microbes available to the plant.\u003c/p>\n\u003cfigure id=\"attachment_23733\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/Compost_grapes_640.jpg\">\u003cimg class=\"size-thumbnail wp-image-23733\" title=\"Compost_grapes_640\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/09/Compost_grapes_640-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Tiny young grapes on a vine at Old Hill Ranch, in Glen Ellen. Photo: Kate Szrom.\u003c/figcaption>\u003c/figure>\n\u003cp>When QUEST visited Old Hill Ranch, it was a hot, sunny June day. There had just been a full moon and the blooms on the vines had set into tiny green grapes.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cfigure id=\"attachment_23409\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/2011/09/01/medical-meditation/at-the-feet-of-an-ancient-master/\" rel=\"attachment wp-att-23409\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/At-the-Feet-of-an-Ancient-Master-300x169.jpg\" alt=\"\" title=\"At the Feet of an Ancient Master \" width=\"300\" height=\"169\" class=\"size-thumbnail wp-image-23409\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">At the Feet of an Ancient Master by Premasagar\u003c/figcaption>\u003c/figure>\n\u003cp>I have the pleasure of attending \u003ca href=\"http://www.booksmith.com/nightcircus\">Bookswap\u003c/a> at the \u003ca href=\"http://\">Booksmith\u003c/a> every other month. Its a meet and greet of the literary sort where we all introduce our favorite book, talk and then swap. At the end of each Bookswap, the Booksmith staff brings out advanced copies of books for guests to peruse. One cover caught my attention the last time I went – \u003cem>Transcendence\u003c/em> by \u003ca href=\"http://normanrosenthal.com/\">Norman E. Rosenthal. M.D.\u003c/a> – a book highlighting Transcendental Meditation from a medical viewpoint.\u003c/p>\n\u003cp>Dr. Rosenthal is a reputable doctor with a twenty-year tenure at the National Institute of Mental Health; he also pioneered the study of seasonal affect disorder (SAD) and wrote about the study in his former book \u003cem>Winter Blues\u003c/em>. He now a clinical professor of psychiatry at Georgetown Medical School and also a seasoned meditator. In this book, he elucidates the practice of transcendental meditation -TM and highlights how it can greatly reduce symptoms of stress, depression, ADHD, impulsiveness, addiction, anxiety, and post traumatic syndrome. He draws from personal accounts spanning environments and conditions, as well as articles detailing clinical research from over 340 peer-reviewed trials.\u003c/p>\n\u003cp>Transcendental Meditation has been the most studied form of meditation. It’s a non-religious meditation consisting of sitting comfortably for twenty minutes with your eyes closed, twice a day while focusing the mind’s eye on a mantra or nonverbal sound to attain a deep state of attentive relaxation. \u003c/p>\n\u003cp>Studies have shown that brain waves achieve coherence during meditation; “which is an area of growing interest among neuroscientists. All the different parts of the brain generate waves in several frequencies. These brain waves are said to be coherent when waves of a given frequency from different parts of the brain are in step with one another…It correlates with high levels of intelligence and competence…To produce a train of thought or execute an action, all the cells have to function as a unit, just as soldiers in battle need to advance in a coordinated way” (Rosenthal, pgs. 21-22).\u003c/p>\n\u003cp>Moreover, TM emanates a deep sense of relaxation that given practice permeates the rest of the day. In our stressful and packed world, it is a vacation from stress twice a day when noise and stress can drift away. Rosenthal explains in \u003cem>Transcendence\u003c/em> that in today’s world we are living more often in the “sympathetic nervous system (SNS), which governs (among other things) an alarm function, the ‘fight-or-flight response’ … the parasympathetic system…relaxes you” (Rosenthal pg 57). This means that anxiety, depression, cardiovascular disease and other maladies have their touchstone in an overrun SNS that create hormones, while in the short term get the body out of harm’s way, in the long run damage the body. Meditation, gets people out of this stressful situation by deep relaxation as both systems cannot be triggered at the same time. \u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>While reading this book, I decided to do my own experiment and start this form of mediation. For the past couple of weeks, I have been meditating twice a day for 10 to 15 minutes, once in the morning and once in the afternoon. I was diagnosed with Attention Deficit Disorder and often struggle with anxiety and distraction. I have weaned off medication for ADD but I still rely heavily on both exercise and Yerba Mate tea to help me focus at work. I have been so much more focused, relaxed and happy these last two weeks. I noticed that instead of responding to a situation with anxiety, I could just make a choice and follow through with little disruption. Even in two weeks, I have noticed a significant improvement in the quality of my life and a reduced stress load. I plan on continuing the practice as I see very little to no side effects and a much better quality of life which was also the clear message I got from reading \u003ca href=\"http://\">\u003cem>Transcendence\u003c/em>\u003c/a>. \u003c/p>\n\n",
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"content": "\u003cfigure id=\"attachment_23340\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/cattle.jpg\">\u003cimg class=\"size-thumbnail wp-image-23340\" title=\"cattle\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/cattle-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">How can California cattle ranches pull carbon out of the atmosphere? Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>What if we could pull carbon dioxide out of the atmosphere and store it underground? Well, plants do this every day—through photosynthesis. Plants take CO2 from the air and incorporate it into their tissues. When their leaves drop to the ground, or bits of their roots slough off, or they die and decompose, the carbon from the plants’ tissues goes into the soil. Researchers from UC Berkeley are working with cattle ranchers in Marin County to figure out how to increase the amount of carbon stored in the soil. I spoke to Berkeley grad student \u003ca href=\"http://nature.berkeley.edu/silverlab/?p=110\">Becca Ryals\u003c/a> to learn more about the \u003ca href=\"http://www.marincarbonproject.org/\">Marin Carbon Project\u003c/a>.\u003c!--more-->\u003c/p>\n\u003cp>Becca and other students in her advisor \u003ca href=\"http://cnr.berkeley.edu/silverlab/\">Whendee Silver’s lab\u003c/a>, in the \u003ca href=\"http://ourenvironment.berkeley.edu/\">Department of Environmental Science, Policy and Management\u003c/a> at Berkeley, had been studying the effects of climate change on the carbon in soil. They were taking soil samples from California’s rangelands to see how much carbon is stored—or sequestered—in the soil, and why carbon storage varies so much from place to place. The cattle ranchers, on whose land the researchers were working, wanted to know how their land management practices could increase carbon sequestration in their soils. The ranchers’ questions were the catalyst for the next step in Becca and her colleagues’ research.\u003c/p>\n\u003cp>They did an experiment to see whether adding compost affects the amount of carbon stored in the soil. They set up a study in 2008 in two places—Nicasio Ranch, in Marin county, and the \u003ca href=\"http://ucanr.org/sites/sfrec/\">Sierra Foothill Research and Extension Center\u003c/a> in the Sierra Valley. At each site, in some areas they added a half-inch thick layer of commercially available compost, made from yard waste and food scraps, to the soil. In other areas, they left the soil alone.\u003c/p>\n\u003cfigure id=\"attachment_23342\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/tractor2.jpg\">\u003cimg class=\"size-full wp-image-23342\" title=\"tractor2\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/tractor2.jpg\" alt=\"\" width=\"640\" height=\"290\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/08/tractor2.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/08/tractor2-400x181.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Compost is added to the soil at a cattle ranch, part of the Marin Carbon Project. Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>When they returned to the plots a few months later, they found that the plots with compost had a 50-70% increase in grass production. The compost had fertilized the grass and increased its growth. The ranchers were happy to see the increase in grass production—there was more forage for their cattle.\u003c/p>\n\u003cfigure id=\"attachment_23343\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg\">\u003cimg class=\"size-full wp-image-23343\" title=\"MarinCarbonExperimentalPlots\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg\" alt=\"\" width=\"640\" height=\"484\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots-400x303.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The boxed areas were treated with a ½ inch layer of compost; the grass there grew thicker for 3 years after the compost was added. Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>Becca and her colleagues expected that after a year, the effect of the compost would have worn off. They were wrong. When they went back the next year, the grass production was still up 50-70%. They went back three years after the compost was added, and they could still see its effects—grass production was still up by 50-70%. The compost acted as a slow-release fertilizer. They’re continuing to monitor the plots: for how long will the compost added in 2008 continue to benefit the grass, the soil, and the ranchers?\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Becca and her colleagues took multiple soil samples from the different plots, and found that in the compost-treated plots the amount of carbon in the soil had increased by about 20%. This is a huge increase in the world of soil carbon. Some of this carbon comes directly from the compost, and some is there because of the increase in grass production—grass dies and the carbon from its tissues enters the soil.\u003c/p>\n\u003cp>\u003ca href=\"http://nature.berkeley.edu/silverlab/?p=635\">Marcia DeLonge\u003c/a>, a post-doc in Becca’s lab, is looking at whether the type of compost matters. She’s comparing the effects of yard waste/food scrap compost and compost made from cow manure—which is readily available at her field sites, three dairies in Marin County. Their work has become well known to local ranchers, and they received offers from so many ranchers to do the study on their land that they had difficulty choosing their field sites.\u003c/p>\n\u003cp>The Marin Carbon Project is starting to talk with ranchers and local agencies about a \u003ca href=\"http://www.marincarbonproject.org/programs.php\">carbon market\u003c/a>—using the researchers’ findings, they can monitor the amount of carbon in the soil, and ranchers can be rewarded for the carbon sequestered on their property.\u003c/p>\n\u003cp>Becca, Whendee, and her lab-mates share their research findings with ranchers through presentations at public venues. The ranchers ask them questions, and the researchers figure out how they can answer them, by designing new studies and asking more questions.\u003c/p>\n\u003cp>Becca enjoys the science: “There are interesting, challenging questions,” she says. But “I really like working with the ranchers and seeing the research findings applied to everyday land management decisions.”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Her work also gives her an appreciation for local food. “When I see Point Reyes Blue Cheese,” Becca says, “I know that rancher. I saw those soils.”\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_23340\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/cattle.jpg\">\u003cimg class=\"size-thumbnail wp-image-23340\" title=\"cattle\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/cattle-300x169.jpg\" alt=\"\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">How can California cattle ranches pull carbon out of the atmosphere? Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>What if we could pull carbon dioxide out of the atmosphere and store it underground? Well, plants do this every day—through photosynthesis. Plants take CO2 from the air and incorporate it into their tissues. When their leaves drop to the ground, or bits of their roots slough off, or they die and decompose, the carbon from the plants’ tissues goes into the soil. Researchers from UC Berkeley are working with cattle ranchers in Marin County to figure out how to increase the amount of carbon stored in the soil. I spoke to Berkeley grad student \u003ca href=\"http://nature.berkeley.edu/silverlab/?p=110\">Becca Ryals\u003c/a> to learn more about the \u003ca href=\"http://www.marincarbonproject.org/\">Marin Carbon Project\u003c/a>.\u003c!--more-->\u003c/p>\n\u003cp>Becca and other students in her advisor \u003ca href=\"http://cnr.berkeley.edu/silverlab/\">Whendee Silver’s lab\u003c/a>, in the \u003ca href=\"http://ourenvironment.berkeley.edu/\">Department of Environmental Science, Policy and Management\u003c/a> at Berkeley, had been studying the effects of climate change on the carbon in soil. They were taking soil samples from California’s rangelands to see how much carbon is stored—or sequestered—in the soil, and why carbon storage varies so much from place to place. The cattle ranchers, on whose land the researchers were working, wanted to know how their land management practices could increase carbon sequestration in their soils. The ranchers’ questions were the catalyst for the next step in Becca and her colleagues’ research.\u003c/p>\n\u003cp>They did an experiment to see whether adding compost affects the amount of carbon stored in the soil. They set up a study in 2008 in two places—Nicasio Ranch, in Marin county, and the \u003ca href=\"http://ucanr.org/sites/sfrec/\">Sierra Foothill Research and Extension Center\u003c/a> in the Sierra Valley. At each site, in some areas they added a half-inch thick layer of commercially available compost, made from yard waste and food scraps, to the soil. In other areas, they left the soil alone.\u003c/p>\n\u003cfigure id=\"attachment_23342\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/tractor2.jpg\">\u003cimg class=\"size-full wp-image-23342\" title=\"tractor2\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/tractor2.jpg\" alt=\"\" width=\"640\" height=\"290\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/08/tractor2.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/08/tractor2-400x181.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Compost is added to the soil at a cattle ranch, part of the Marin Carbon Project. Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>When they returned to the plots a few months later, they found that the plots with compost had a 50-70% increase in grass production. The compost had fertilized the grass and increased its growth. The ranchers were happy to see the increase in grass production—there was more forage for their cattle.\u003c/p>\n\u003cfigure id=\"attachment_23343\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg\">\u003cimg class=\"size-full wp-image-23343\" title=\"MarinCarbonExperimentalPlots\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg\" alt=\"\" width=\"640\" height=\"484\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/08/MarinCarbonExperimentalPlots-400x303.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The boxed areas were treated with a ½ inch layer of compost; the grass there grew thicker for 3 years after the compost was added. Photo courtesy of Becca Ryals.\u003c/figcaption>\u003c/figure>\n\u003cp>Becca and her colleagues expected that after a year, the effect of the compost would have worn off. They were wrong. When they went back the next year, the grass production was still up 50-70%. They went back three years after the compost was added, and they could still see its effects—grass production was still up by 50-70%. The compost acted as a slow-release fertilizer. They’re continuing to monitor the plots: for how long will the compost added in 2008 continue to benefit the grass, the soil, and the ranchers?\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cfigure id=\"attachment_23286\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2011/08/29/how-neanderthal-are-you/percneanderthal/\" rel=\"attachment wp-att-23286\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/08/PercNeanderthal.jpg\" alt=\"\" title=\"PercNeanderthal\" width=\"640\" height=\"360\" class=\"size-full wp-image-23286\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/08/PercNeanderthal.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/08/PercNeanderthal-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">These results from the \"Interpretome\" tool show that there is a bit of a Neanderthal in me.\u003c/figcaption>\u003c/figure>\n\u003cp>Asking someone if they were a Neanderthal used to be an insult but is now kind of a valid question. If you have any Europeans, Asians or Native Americans in your family tree, odds are there is a \u003ca href=\"http://ww2.kqed.org/quest/2010/05/24/my-3000th-great-grandpa-was-a-neanderthal/\">bit of Neanderthal\u003c/a> in there as well.\u003c/p>\n\u003cp>As one of the whitest people on the planet, I almost certainly have mostly European ancestors. And if I had any doubts, my 23andMe ancestry results confirm the obvious…I am European through and through.\u003c/p>\n\u003cp>This means there is almost certainly some Neanderthal DNA squirreled away in my genome. But how much? I decided to try to find out.\u003c/p>\n\u003cp>First I asked \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>. They quickly replied that they didn’t do that, sorry. So as often happens, I needed to take my genome on a jaunt through the internet to find a tool that could give me the answer I was looking for.\u003c/p>\n\u003cp>I first went to my favorite, \u003ca href=\"http://www.snpedia.com/index.php/SNPedia\">SNPedia\u003c/a>. No luck though. Just a piece about the \u003ca href=\"http://www.thetech.org/genetics/news.php?id=67\">Neanderthal red hair version of the MC1R gene\u003c/a> that hasn’t yet been found in humans. \u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Then I remembered a discussion at Stanford about which professor was genetically the most Neanderthal. Obviously they must have a way of figuring this out. \u003c/p>\n\u003cp>So I contacted Dr. Mike Snyder and he led me to Konrad Karczewski, a graduate student at Stanford. And he directed me to a tool called the \u003ca href=\"http://esquilax.stanford.edu/#start\">Interpretome \u003c/a>that he and some other Stanford folks had developed for their \u003ca href=\"http://stanford.edu/class/gene210/web/html/welcome.html\">personalized medicine class\u003c/a>.\u003c/p>\n\u003cp>This tool has a lot of cool features (feel free to explore) but I headed straight for the Neanderthal section. I plugged in my 23andMe raw data and out popped my results. There are definitely some Neanderthals in my family tree!\u003c/p>\n\u003cp>The site looks at 42 different markers and since we have two copies of each, there are 84 possible Neanderthal hits. I scored a 7 out of 84.\u003c/p>\n\u003cp>Now, since I don’t know if that is a lot, I asked Konrad about the kinds of ranges he sees. He said the average European has a score of around 7-10 which puts me at the lower end of average. He also said that someone in an online forum had reported a 26 but the highest Konrad had ever seen with his own eyes was 20. And that the lowest he has seen for Europeans or Asians was around 3-5.\u003c/p>\n\u003cp>So there you have it. I am on the low end of Neanderthalness for someone of European descent using these 42 \u003ca href=\"https://www.23andme.com/gen101/snps/\">SNPs\u003c/a>. And less Neanderthal than a number of Stanford professors!\u003c/p>\n\u003cp>How cool are genetics when it lets me figure out that I am definitely a bit Neanderthal but not as Neanderthal as certain unnamed Stanford professors? \u003c/p>\n\u003cp>\u003cstrong>More Information\u003c/strong>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://www.thetech.org/genetics/news.php?id=128\">Neanderthals and you.\u003c/a>\u003c/p>\n\n",
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"content": "\u003cp>If you ever want to meet someone enthusiastic about their job, catch up with the staff that works in the \u003ca href=\"http://www.omahazoo.com/exhibits/butterfly-insect-pavilion/\">Omaha Henry Doorly Zoo Butterfly and Insect Pavilion\u003c/a>. The first time I visited to discuss videotaping with them for the \u003ca href=\"http://www.fws.gov/mountain-prairie/species/invertebrates/saltcreektiger/FinalRecoveryOutlineFeb2009.pdf\">Salt Creek tiger beetle recovery project\u003c/a>, they brought out bug after bug for me to see. These insects didn't have anything to do with Salt Creek tiger beetles, but Kay Klatt and her staff wanted me to see the amazing features that different bugs have.\u003c/p>\n\u003cp>There's the \u003ca href=\"http://en.wikipedia.org/wiki/Atlas_beetle\">atlas beetle\u003c/a> that's black and shiny like a newly washed Harley Davidson motorcycle. There's \u003ca href=\"http://en.wikipedia.org/wiki/Leaf-cutter_ants\">leafcutter ants\u003c/a> that slice leaves off of trees with a cut as clean as a butcher's knife would make. (Those leaves become fungi, which is actually what they eat.) I'd never seen anything like a \u003ca href=\"http://en.wikipedia.org/wiki/Gongylus_gongylodes\">violin mantis\u003c/a> before. This bark-colored creature flexes at the joints as it moves to make it seem more like a robot.\u003c/p>\n\u003cp>\"Eewww!!\" That's what a lot of people say when they see bugs. Kay Klatt, Supervisor of the Butterfly and Insect Pavilion at Omaha's Henry Doorly Zoo, says, \"That's perfect. That's what gets people interested, especially young people. What is that? What does it do? How does that work? That's what might motivate someone to want to work with insects when they grow up.\"\u003c/p>\n\u003cp>The staff couldn't stop telling me about the creatures as they showed them to me. They talked about how many times they've been bitten or what species have bitten them, but they even did that with enthusiasm. I learned a lot about many types of bugs in a short amount of time. But the other thing I learned is that rare and fragile creatures like \u003ca href=\"http://drshigley.com/lgh/sctb/\">Salt Creek tiger beetles\u003c/a> are in good hands when people like this are looking out for them. The odds are stacked against \u003ca href=\"http://www.fws.gov/mountain-prairie/species/invertebrates/saltcreektiger/\">the tiger beetles\u003c/a>, but if they make it, it will be because there are people with a passion to help them.\u003c/p>\n\u003cp>The passion will be a test of patience for the next several months. All the staff can do with the Salt Creek tiger beetle larvae is feed it. To do that, its food is placed at the top of a tube of soil, then the larvae will come to the top to get it. I was surprised to learn that's about all the staff can do -- watch and wait until (hopefully) the larvae turn into beetles and then can be released into saline habitats near Lincoln next spring.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003ciframe src=\"http://kqed03.streamguys.us/anon.kqed/slideshow/Tiger_Beetle_Slideshow/_files/iframe.html?noscale=640x423\" width=\"640\" height=\"423\" scrolling=\"no\" frameborder=\"0\">\u003c/iframe>\u003c/p>\n\u003cp>The Salt Creek tiger beetle is one of the most endangered species in the United States, with only two to five hundred beetles left. They're found only in a small saline wetland area just north of Lincoln, Nebraska. We visited the wetland with Mitch Paine, a former research assistant at the University of Nebraska, Lincoln who worked with the beetles and comes back every summer to photograph the Salt Creek tiger beetles.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>Produced by Diego Moreno / QUEST Nebraska. Beetle photographs by Mitch Paine.\u003c/em>\u003c/p>\n\n",
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"info": "Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. Together in Possible, Hoffman and Finger lead enlightening discussions about building a brighter collective future. The show features interviews with visionary guests like Trevor Noah, Sam Altman and Janette Sadik-Khan. Possible paints an optimistic portrait of the world we can create through science, policy, business, art and our shared humanity. It asks: What if everything goes right for once? How can we get there? Each episode also includes a short fiction story generated by advanced AI GPT-4, serving as a thought-provoking springboard to speculate how humanity could leverage technology for good.",
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"soldout": {
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"title": "SOLD OUT: Rethinking Housing in America",
"tagline": "A new future for housing",
"info": "Sold Out: Rethinking Housing in America",
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