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"disqusTitle": "Debate Over on Climate Change, Says Chief UN Climate Negotiator ",
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"content": "\u003ch2>\u003c/h2>\n\u003cfigure id=\"attachment_55193\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg\">\u003cimg class=\"size-full wp-image-55193\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg\" alt=\"Photo by Tom Hawk\" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003cem>Watching the golden toad disappear from Costa Rican rainforests had a lasting impression on Figueres. Photo by Tom Hawk\u003c/em>\u003c/figcaption>\u003c/figure>\n\u003ch2>\u003cspan style=\"color: #888888\">\u003cstrong>An Expert Opinion: \u003c/strong>\u003c/span>\u003cstrong>Christiana Figueres\u003c/strong>\u003c/h2>\n\u003cp>\u003cstrong>\u003cem>Hailing from a family with two former presidents of Costa Rica, Christiana Figueres was primed to tackle daunting political challenges, head on. Figueres first found her footing as the founder of the Center for Sustainable Development in the Americas. Now, as the executive secretary of the \u003c/em>\u003ca href=\"http://unfccc.int/2860.php\">\u003cem>United Nations Framework Convention on Climate Change\u003c/em>\u003c/a>\u003cem>, she travels internationally helping countries agree upon strategies to limit greenhouse gas emissions.\u003c/em>\u003c/strong>\u003cstrong>\u003cem> On \u003cstrong>\u003cem>a recent visit to San Francisco, she attended a \u003ca href=\"http://www.cvent.com/events/navigating-the-american-carbon-world/event-summary-370741f03c8c4363b1865ec6bb8e96c3.aspx?i=b980a317-eb6f-4eb5-b6bd-57c1a0437b45\">carbon market conference\u003c/a> to talk about California's cap and trade program, which went into effect last year.\u003c/em>\u003c/strong>\u003c/em>\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_55207\" class=\"wp-caption alignleft\" style=\"max-width: 184px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Figueres-profile-resized.jpg\">\u003cimg class=\"wp-image-55207 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Figueres-profile-resized.jpg\" alt=\"Figueres profile resized\" width=\"184\" height=\"245\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized.jpg 1417w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-400x534.jpg 400w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-800x1067.jpg 800w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-1180x1574.jpg 1180w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-960x1280.jpg 960w\" sizes=\"(max-width: 184px) 100vw, 184px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Figueres has been the executive secretary of the UNFCCC since 2010\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>What is your role with the U.N. and what are in you in town for?\u003c/strong>\u003c/p>\n\u003cp>[My role is] to support governments in their ongoing efforts to reach agreements with each other about how they’re going to address climate change. I’m in California to recognize California’s leadership with their \u003ca href=\"http://ww2.kqed.org/quest/audio/cap-and-trade-101-how-californias-carbon-market-works/\">cap and trade program\u003c/a> because it is quite unique for the U.S. that a state has moved forward with a market-based solution to their climate policy. Covering 85 percent of the state's greenhouse gas emissions, and second in size only to the European Union system, the robustness of California's program cannot be denied.\u003c/p>\n\u003cp>\u003cstrong>What is the value of California’s leadership if there are so few followers? Isn’t there a danger that it’s all going to be too little too late?\u003c/strong>\u003c/p>\n\u003cp>Yes, there is that danger but that’s not the only possibility. We have so many more extreme weather events that are really making this issue no longer a debate. Every single country is being affected and every single country is realizing that—in their own interest—they need to address this. There is no more compelling evidence of this than the joint working group between the United States and China. If you had asked anybody four years ago, three years ago, two years ago: will the United States and China ever come to the table on climate change to try to find joint collaborative solutions, it would have been a hard sell to say yes. Here we have a joint working group of the United States and China, not because they necessarily are looking at the global benefit, but because they are motivated by avoiding the national impacts that they are already seeing.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>So you think cap and trade can work as a policy? \u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_55248\" class=\"wp-caption alignright\" style=\"max-width: 362px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/goldenToadMap.jpg\">\u003cimg class=\" wp-image-55248 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/goldenToadMap.jpg\" alt=\"Last seen in 1989, the golden toad is thouught to be extinct due to climate change and disease. Photo courtesy of Conservation International\" width=\"362\" height=\"294\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/goldenToadMap.jpg 603w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/goldenToadMap-400x325.jpg 400w\" sizes=\"(max-width: 362px) 100vw, 362px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Last seen in 1989, the golden toad is thought to be extinct due to climate change and disease. Photo courtesy of Conservation International\u003c/figcaption>\u003c/figure>\n\u003cp>Absolutely, it has been proven to work in the \u003ca href=\"http://europa.eu/about-eu/index_en.htm\">European Union\u003c/a>, that is the oldest cap and trade system, and it is a model that is being experimented with in many other countries as well. So yes, I think it is a policy of choice that will be used by many countries, and many subnational governments.\u003c/p>\n\u003cp>\u003cstrong>Many would suggest that with the pace of climate change, that there’s just no way we’re going to reign in warming at the two-degree level, what’s your take on that?\u003c/strong>\u003c/p>\n\u003cp>There have been, over the past 12 months, at least four studies that have looked at this issue and looked at the fact that greenhouse gas emissions continue to rise and that should this continue as a business as usual scenario, that it would be impossible to reach that two-degree target. However, every single one of those studies also says that there is no reason why we have to continue along that business as usual route. Every single one of those studies says we have number one, the technology, number two, the capital and number three, the human ingenuity to change business as usual and make a serious dent in addressing climate change. So I still am heartened that we will be able to do that.\u003c/p>\n\u003cp>\u003cstrong>Was environmental sustainability something that you remember discussing around the family dinner table at an early age?\u003c/strong>\u003c/p>\n\u003cp>At the dinner table--no, because I don’t think the concept of sustainability was something that was around in the 1960s and ’70s. That came later. What was always a discussion at the dinner table was how do you structure societies and economic systems in order to benefit those that are most vulnerable. That is not very different from what we’re doing in the climate arena. It’s very clear that there are a group of countries that are least responsible for climate change and they are the most vulnerable. The \u003ca href=\"http://aosis.org/\">low-lying island states\u003c/a> are those that have the least responsibility and they are the most vulnerable because of \u003ca href=\"http://www.csc.noaa.gov/digitalcoast/tools/slrviewer/\">sea level rise\u003c/a>. And so our progress and our success in meeting climate change needs to be measured against how well are we protecting the future of those that are most vulnerable.\u003c/p>\n\u003cp>\u003cstrong>Climate change is unlike other environmental issues because it’s intangible. What’s—\u003c/strong>\u003c/p>\n\u003cp>[INTERRUPTS]\u003cstrong> \u003c/strong>Intangible? It is anything but intangible. Tangible is \u003ca href=\"http://www.srh.noaa.gov/mfl/?n=sandy\">[Hurricane] Sandy\u003c/a>, tangible is sea level rise that is completely swamping populations. Tangible is the fact that the farming belt in the United States went bankrupt last year and that had a huge \u003ca href=\"http://www.worldbank.org/en/news/press-release/2012/08/30/severe-droughts-drive-food-prices-higher-threatening-poor\">spike in food prices\u003c/a> across the world. So it’s very tangible, it’s just very distributed across the world. In that sense it’s difficult to pinpoint with one single finger because the effects are not just seen in one single country, they are seen everywhere.\u003cstrong> \u003c/strong>\u003c/p>\n\u003cp>\u003cstrong>When was first time you feel like you really saw the impact of climate change?\u003c/strong>\u003c/p>\n\u003cp>I was about 12 or 13 and my parents took me to a rainforest in Costa Rica where there was an endemic \u003ca href=\"http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=D00A\">golden frog\u003c/a> that was a beautiful species. By the time I was married and had children, the species of frog had disappeared because of the increasing temperatures [caused by climate change]. The fact that I have seen the disappearance of a species in my lifetime has left me marked. I now realize that the planet I am leaving to my children is visibly diminished from the planet I inherited.\u003c/p>\n\u003cp>\u003cstrong>To that point, what would you say to students—the generations that will inherit the problems we’re facing now?\u003c/strong>\u003c/p>\n\u003cp>They’re going to have to finish fixing this problem. The only things we oldies can do right now is identify the possibilities of what the solutions will be, but there is no doubt we’re handing over a very serious problem to the next generation and they’re going to have to step up and be the ones that finish the solution.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003cstrong>\u003cem>*This interview has been condensed and edited. Science Editor Craig Miller contributed to this story.\u003c/em>\u003c/strong>\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003ch2>\u003c/h2>\n\u003cfigure id=\"attachment_55193\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg\">\u003cimg class=\"size-full wp-image-55193\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg\" alt=\"Photo by Tom Hawk\" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Frog-Golden-Toad-sized-correctly-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003cem>Watching the golden toad disappear from Costa Rican rainforests had a lasting impression on Figueres. Photo by Tom Hawk\u003c/em>\u003c/figcaption>\u003c/figure>\n\u003ch2>\u003cspan style=\"color: #888888\">\u003cstrong>An Expert Opinion: \u003c/strong>\u003c/span>\u003cstrong>Christiana Figueres\u003c/strong>\u003c/h2>\n\u003cp>\u003cstrong>\u003cem>Hailing from a family with two former presidents of Costa Rica, Christiana Figueres was primed to tackle daunting political challenges, head on. Figueres first found her footing as the founder of the Center for Sustainable Development in the Americas. Now, as the executive secretary of the \u003c/em>\u003ca href=\"http://unfccc.int/2860.php\">\u003cem>United Nations Framework Convention on Climate Change\u003c/em>\u003c/a>\u003cem>, she travels internationally helping countries agree upon strategies to limit greenhouse gas emissions.\u003c/em>\u003c/strong>\u003cstrong>\u003cem> On \u003cstrong>\u003cem>a recent visit to San Francisco, she attended a \u003ca href=\"http://www.cvent.com/events/navigating-the-american-carbon-world/event-summary-370741f03c8c4363b1865ec6bb8e96c3.aspx?i=b980a317-eb6f-4eb5-b6bd-57c1a0437b45\">carbon market conference\u003c/a> to talk about California's cap and trade program, which went into effect last year.\u003c/em>\u003c/strong>\u003c/em>\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_55207\" class=\"wp-caption alignleft\" style=\"max-width: 184px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Figueres-profile-resized.jpg\">\u003cimg class=\"wp-image-55207 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Figueres-profile-resized.jpg\" alt=\"Figueres profile resized\" width=\"184\" height=\"245\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized.jpg 1417w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-400x534.jpg 400w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-800x1067.jpg 800w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-1180x1574.jpg 1180w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Figueres-profile-resized-960x1280.jpg 960w\" sizes=\"(max-width: 184px) 100vw, 184px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Figueres has been the executive secretary of the UNFCCC since 2010\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>What is your role with the U.N. and what are in you in town for?\u003c/strong>\u003c/p>\n\u003cp>[My role is] to support governments in their ongoing efforts to reach agreements with each other about how they’re going to address climate change. I’m in California to recognize California’s leadership with their \u003ca href=\"http://ww2.kqed.org/quest/audio/cap-and-trade-101-how-californias-carbon-market-works/\">cap and trade program\u003c/a> because it is quite unique for the U.S. that a state has moved forward with a market-based solution to their climate policy. Covering 85 percent of the state's greenhouse gas emissions, and second in size only to the European Union system, the robustness of California's program cannot be denied.\u003c/p>\n\u003cp>\u003cstrong>What is the value of California’s leadership if there are so few followers? Isn’t there a danger that it’s all going to be too little too late?\u003c/strong>\u003c/p>\n\u003cp>Yes, there is that danger but that’s not the only possibility. We have so many more extreme weather events that are really making this issue no longer a debate. Every single country is being affected and every single country is realizing that—in their own interest—they need to address this. There is no more compelling evidence of this than the joint working group between the United States and China. If you had asked anybody four years ago, three years ago, two years ago: will the United States and China ever come to the table on climate change to try to find joint collaborative solutions, it would have been a hard sell to say yes. Here we have a joint working group of the United States and China, not because they necessarily are looking at the global benefit, but because they are motivated by avoiding the national impacts that they are already seeing.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>So you think cap and trade can work as a policy? \u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_55248\" class=\"wp-caption alignright\" style=\"max-width: 362px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/goldenToadMap.jpg\">\u003cimg class=\" wp-image-55248 \" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/goldenToadMap.jpg\" alt=\"Last seen in 1989, the golden toad is thouught to be extinct due to climate change and disease. Photo courtesy of Conservation International\" width=\"362\" height=\"294\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/goldenToadMap.jpg 603w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/goldenToadMap-400x325.jpg 400w\" sizes=\"(max-width: 362px) 100vw, 362px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Last seen in 1989, the golden toad is thought to be extinct due to climate change and disease. Photo courtesy of Conservation International\u003c/figcaption>\u003c/figure>\n\u003cp>Absolutely, it has been proven to work in the \u003ca href=\"http://europa.eu/about-eu/index_en.htm\">European Union\u003c/a>, that is the oldest cap and trade system, and it is a model that is being experimented with in many other countries as well. So yes, I think it is a policy of choice that will be used by many countries, and many subnational governments.\u003c/p>\n\u003cp>\u003cstrong>Many would suggest that with the pace of climate change, that there’s just no way we’re going to reign in warming at the two-degree level, what’s your take on that?\u003c/strong>\u003c/p>\n\u003cp>There have been, over the past 12 months, at least four studies that have looked at this issue and looked at the fact that greenhouse gas emissions continue to rise and that should this continue as a business as usual scenario, that it would be impossible to reach that two-degree target. However, every single one of those studies also says that there is no reason why we have to continue along that business as usual route. Every single one of those studies says we have number one, the technology, number two, the capital and number three, the human ingenuity to change business as usual and make a serious dent in addressing climate change. So I still am heartened that we will be able to do that.\u003c/p>\n\u003cp>\u003cstrong>Was environmental sustainability something that you remember discussing around the family dinner table at an early age?\u003c/strong>\u003c/p>\n\u003cp>At the dinner table--no, because I don’t think the concept of sustainability was something that was around in the 1960s and ’70s. That came later. What was always a discussion at the dinner table was how do you structure societies and economic systems in order to benefit those that are most vulnerable. That is not very different from what we’re doing in the climate arena. It’s very clear that there are a group of countries that are least responsible for climate change and they are the most vulnerable. The \u003ca href=\"http://aosis.org/\">low-lying island states\u003c/a> are those that have the least responsibility and they are the most vulnerable because of \u003ca href=\"http://www.csc.noaa.gov/digitalcoast/tools/slrviewer/\">sea level rise\u003c/a>. And so our progress and our success in meeting climate change needs to be measured against how well are we protecting the future of those that are most vulnerable.\u003c/p>\n\u003cp>\u003cstrong>Climate change is unlike other environmental issues because it’s intangible. What’s—\u003c/strong>\u003c/p>\n\u003cp>[INTERRUPTS]\u003cstrong> \u003c/strong>Intangible? It is anything but intangible. Tangible is \u003ca href=\"http://www.srh.noaa.gov/mfl/?n=sandy\">[Hurricane] Sandy\u003c/a>, tangible is sea level rise that is completely swamping populations. Tangible is the fact that the farming belt in the United States went bankrupt last year and that had a huge \u003ca href=\"http://www.worldbank.org/en/news/press-release/2012/08/30/severe-droughts-drive-food-prices-higher-threatening-poor\">spike in food prices\u003c/a> across the world. So it’s very tangible, it’s just very distributed across the world. In that sense it’s difficult to pinpoint with one single finger because the effects are not just seen in one single country, they are seen everywhere.\u003cstrong> \u003c/strong>\u003c/p>\n\u003cp>\u003cstrong>When was first time you feel like you really saw the impact of climate change?\u003c/strong>\u003c/p>\n\u003cp>I was about 12 or 13 and my parents took me to a rainforest in Costa Rica where there was an endemic \u003ca href=\"http://ecos.fws.gov/speciesProfile/profile/speciesProfile.action?spcode=D00A\">golden frog\u003c/a> that was a beautiful species. By the time I was married and had children, the species of frog had disappeared because of the increasing temperatures [caused by climate change]. The fact that I have seen the disappearance of a species in my lifetime has left me marked. I now realize that the planet I am leaving to my children is visibly diminished from the planet I inherited.\u003c/p>\n\u003cp>\u003cstrong>To that point, what would you say to students—the generations that will inherit the problems we’re facing now?\u003c/strong>\u003c/p>\n\u003cp>They’re going to have to finish fixing this problem. The only things we oldies can do right now is identify the possibilities of what the solutions will be, but there is no doubt we’re handing over a very serious problem to the next generation and they’re going to have to step up and be the ones that finish the solution.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>\u003cem>*This interview has been condensed and edited. Science Editor Craig Miller contributed to this story.\u003c/em>\u003c/strong>\u003c/p>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Fish Earbones Provide a Rare Glimpse into the Past and Future of Fisheries",
"title": "Fish Earbones Provide a Rare Glimpse into the Past and Future of Fisheries",
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"content": "\u003cfigure id=\"attachment_55023\" class=\"wp-caption aligncenter\" style=\"max-width: 628px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/3067134212_b217e2bd81_z-2/\" rel=\"attachment wp-att-55023\">\u003cimg class=\"size-full wp-image-55023\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273.jpg\" alt=\"The rings on an otolith Photo courtesy of Flickr user Eustatic Creative Commons license\" width=\"628\" height=\"358\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273.jpg 628w, https://ww2.kqed.org/app/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273-400x228.jpg 400w\" sizes=\"(max-width: 628px) 100vw, 628px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The rings on an otolith: photo courtesy of \u003ca href=\"http://www.flickr.com/photos/eustatic/3067134212/\">Eustatic\u003c/a>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003ccode>\u003cbr>\n\u003c/code>\u003c/p>\n\u003cp>\u003cem>\u003cstrong>\u003cspan style=\"color: #888888\">Field Notes\u003c/span>\u003cspan style=\"color: #888888\">\u003cstrong>:\u003c/strong> \u003c/span>\u003cspan style=\"color: #000000\">Cathy Britt, The Burke Museum\u003c/span>\u003c/strong>\u003c/em>\u003c/p>\n\u003cp>From salmon steaks and sushi, to fish nuggets and crab cakes, the world’s fisheries provide three billion people with nearly 15 percent of their average animal protein intake. The numerous fish, crab, shrimp, and shellfish that live in these cold, productive waters make Alaska and the Pacific Northwest essentially the biggest seafood market in the world. Pollock from the Bering Sea is a staple, found in fish sticks and fillets for fast-food sandwiches.\u003c/p>\n\u003cp>To ensure that future generations will continue to enjoy the benefits of these fisheries, they must be sustainably managed. This is where science and management come into play.\u003c/p>\n\u003cp>As graduate researcher Jeremy Harris puts it, “We know what can happen to fish with too much fishing, but I want to learn if we can spot this when it’s first starting to happen and set limits and regulations that prevent it.” Harris, a University of Washington graduate researcher, is turning to a collection of pollock otoliths (A.K.A ear bones) at the \u003ca href=\"http://www.burkemuseum.org/\">Burke Museum of Natural History and Culture\u003c/a> for insights into how much fishing is too much.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Finding Answers in Unexpected Places\u003c/h2>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/jeremyholdingotolith/\" rel=\"attachment wp-att-54276\">\u003cimg class=\"wp-image-54276 alignleft\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/JeremyHoldingOtolith-e1368141930563-292x253.jpg\" alt=\"JeremyHoldingOtolith\" width=\"182\" height=\"157\">\u003c/a>\u003c/p>\n\u003cp>Many people wonder why natural history museums hold onto \"all that old stuff\" in their research collections. Well sometimes, all that old stuff can hold information critical to understanding our world. It's just a question of waiting until science matures enough to decode the information they hold. The Burke Museum’s collection of pollock otoliths is a great example.\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Otoliths Archive Ocean Data\u003c/h2>\n\u003cp>[jwplayer config=\"QUEST Video Player Inline II\" mediaid=\"65346\"]\u003cbr>\nSimilar to the rings in a tree, otolith layers form rings that can be counted and measured to determine the fish’s age and growth over the years of its life. Most fish have three otoliths, commonly referred to as ear bones, at the rear of their skull to aid in balance, orientation and hearing. Otoliths are actually stone-like composites that develop layers of proteins and calcium carbonate from the fish’s birth until its death – offering a record of age, growth rate and reproductive age, as well as information about water conditions and climate change the fish experienced. Some fish, like rockfish, can live more than 100 years, giving researchers a rare glimpse into environments from more than a century ago.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/oldestotolith/\" rel=\"attachment wp-att-54481\">\u003cimg class=\"alignleft wp-image-54481\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/OldestOtolith-e1368141494119-380x253.jpg\" alt=\"Oldest Otolith\" width=\"304\" height=\"202\">\u003c/a>Thomas Helser, program director at the \u003ca href=\"http://www.afsc.noaa.gov/default.htm\">NOAA’s Alaska Fisheries Science Center\u003c/a> (AFSC) \u003ca href=\"http://www.afsc.noaa.gov/REFM/Age/\">Age and Growth Program\u003c/a>, leads a team of experts in accessing the data within these fish “flight recorders,” as he describes them. Helser and his staff are collaborating with numerous governmental and academic colleagues in the fields of ecology, geology, evolutionary biology and archeology to explore cutting edge technologies that shed light on critical issues like climate change and overfishing. The team processes some otolith samples intensively for geochemical data. Others they cut in half, polish and lightly burn to enhance the rings, then count the rings to estimate age. Annual growth widths are measured to examine changes in growth over time.\u003c/p>\n\u003cp>\u003cstrong>\u003cbr>\n\u003c/strong>\u003c/p>\n\u003ch2>Man-made evolution\u003c/h2>\n\u003cp>[jwplayer config=\"QUEST Video Player Inline II\" mediaid=\"65350\"]\u003cbr>\nFor his research into sustainable fishing levels, Jeremy plans to sample more than 500 Alaska pollock otoliths collected as far back as the 1960s to look for changes in age, growth rate and reproductive age of the fish over time. Overfishing can cause fish to mature faster and reproduce at a younger age as a means to compensate for loss of reproductive capacity. This may eventually cause an evolutionary change through removing genetic traits associated with older, larger, more valuable fish.\u003c/p>\n\u003cp>Jeremy will pair what he learns from the otolith collection with population and environmental data collected by a range of people and organizations, to gain a deeper understanding of the relationship between the size and age of mature fish, and the volume of fishing happening at the time. “I hope to put this issue on the radar so people start thinking about longer-term evolutionary impacts of fishing,” says Jeremy.\u003c/p>\n\u003cp>Thanks to a grant from the National Science Foundation, Jeremy is also helping to transfer more than two million otoliths collected by NOAA over the past 50 years to their new, permanent home as part of the Burke Museum’s fish collection. There they will be held safely, until the day that science finds a new way to unlock their precious data.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/jeremyincollection/\" rel=\"attachment wp-att-54277\">\u003cimg class=\"aligncenter size-full wp-image-54277\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578.jpg\" alt=\"Jeremy In Collection\" width=\"640\" height=\"427\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578-400x267.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003c/p>\n\u003cp> \u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_55023\" class=\"wp-caption aligncenter\" style=\"max-width: 628px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/3067134212_b217e2bd81_z-2/\" rel=\"attachment wp-att-55023\">\u003cimg class=\"size-full wp-image-55023\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273.jpg\" alt=\"The rings on an otolith Photo courtesy of Flickr user Eustatic Creative Commons license\" width=\"628\" height=\"358\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273.jpg 628w, https://ww2.kqed.org/app/uploads/sites/39/2013/03/3067134212_b217e2bd81_z-e1369175284273-400x228.jpg 400w\" sizes=\"(max-width: 628px) 100vw, 628px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The rings on an otolith: photo courtesy of \u003ca href=\"http://www.flickr.com/photos/eustatic/3067134212/\">Eustatic\u003c/a>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003ccode>\u003cbr>\n\u003c/code>\u003c/p>\n\u003cp>\u003cem>\u003cstrong>\u003cspan style=\"color: #888888\">Field Notes\u003c/span>\u003cspan style=\"color: #888888\">\u003cstrong>:\u003c/strong> \u003c/span>\u003cspan style=\"color: #000000\">Cathy Britt, The Burke Museum\u003c/span>\u003c/strong>\u003c/em>\u003c/p>\n\u003cp>From salmon steaks and sushi, to fish nuggets and crab cakes, the world’s fisheries provide three billion people with nearly 15 percent of their average animal protein intake. The numerous fish, crab, shrimp, and shellfish that live in these cold, productive waters make Alaska and the Pacific Northwest essentially the biggest seafood market in the world. Pollock from the Bering Sea is a staple, found in fish sticks and fillets for fast-food sandwiches.\u003c/p>\n\u003cp>To ensure that future generations will continue to enjoy the benefits of these fisheries, they must be sustainably managed. This is where science and management come into play.\u003c/p>\n\u003cp>As graduate researcher Jeremy Harris puts it, “We know what can happen to fish with too much fishing, but I want to learn if we can spot this when it’s first starting to happen and set limits and regulations that prevent it.” Harris, a University of Washington graduate researcher, is turning to a collection of pollock otoliths (A.K.A ear bones) at the \u003ca href=\"http://www.burkemuseum.org/\">Burke Museum of Natural History and Culture\u003c/a> for insights into how much fishing is too much.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Finding Answers in Unexpected Places\u003c/h2>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/jeremyholdingotolith/\" rel=\"attachment wp-att-54276\">\u003cimg class=\"wp-image-54276 alignleft\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/JeremyHoldingOtolith-e1368141930563-292x253.jpg\" alt=\"JeremyHoldingOtolith\" width=\"182\" height=\"157\">\u003c/a>\u003c/p>\n\u003cp>Many people wonder why natural history museums hold onto \"all that old stuff\" in their research collections. Well sometimes, all that old stuff can hold information critical to understanding our world. It's just a question of waiting until science matures enough to decode the information they hold. The Burke Museum’s collection of pollock otoliths is a great example.\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Otoliths Archive Ocean Data\u003c/h2>\n\u003cp>[jwplayer config=\"QUEST Video Player Inline II\" mediaid=\"65346\"]\u003cbr>\nSimilar to the rings in a tree, otolith layers form rings that can be counted and measured to determine the fish’s age and growth over the years of its life. Most fish have three otoliths, commonly referred to as ear bones, at the rear of their skull to aid in balance, orientation and hearing. Otoliths are actually stone-like composites that develop layers of proteins and calcium carbonate from the fish’s birth until its death – offering a record of age, growth rate and reproductive age, as well as information about water conditions and climate change the fish experienced. Some fish, like rockfish, can live more than 100 years, giving researchers a rare glimpse into environments from more than a century ago.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/oldestotolith/\" rel=\"attachment wp-att-54481\">\u003cimg class=\"alignleft wp-image-54481\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/OldestOtolith-e1368141494119-380x253.jpg\" alt=\"Oldest Otolith\" width=\"304\" height=\"202\">\u003c/a>Thomas Helser, program director at the \u003ca href=\"http://www.afsc.noaa.gov/default.htm\">NOAA’s Alaska Fisheries Science Center\u003c/a> (AFSC) \u003ca href=\"http://www.afsc.noaa.gov/REFM/Age/\">Age and Growth Program\u003c/a>, leads a team of experts in accessing the data within these fish “flight recorders,” as he describes them. Helser and his staff are collaborating with numerous governmental and academic colleagues in the fields of ecology, geology, evolutionary biology and archeology to explore cutting edge technologies that shed light on critical issues like climate change and overfishing. The team processes some otolith samples intensively for geochemical data. Others they cut in half, polish and lightly burn to enhance the rings, then count the rings to estimate age. Annual growth widths are measured to examine changes in growth over time.\u003c/p>\n\u003cp>\u003cstrong>\u003cbr>\n\u003c/strong>\u003c/p>\n\u003ch2>Man-made evolution\u003c/h2>\n\u003cp>[jwplayer config=\"QUEST Video Player Inline II\" mediaid=\"65350\"]\u003cbr>\nFor his research into sustainable fishing levels, Jeremy plans to sample more than 500 Alaska pollock otoliths collected as far back as the 1960s to look for changes in age, growth rate and reproductive age of the fish over time. Overfishing can cause fish to mature faster and reproduce at a younger age as a means to compensate for loss of reproductive capacity. This may eventually cause an evolutionary change through removing genetic traits associated with older, larger, more valuable fish.\u003c/p>\n\u003cp>Jeremy will pair what he learns from the otolith collection with population and environmental data collected by a range of people and organizations, to gain a deeper understanding of the relationship between the size and age of mature fish, and the volume of fishing happening at the time. “I hope to put this issue on the radar so people start thinking about longer-term evolutionary impacts of fishing,” says Jeremy.\u003c/p>\n\u003cp>Thanks to a grant from the National Science Foundation, Jeremy is also helping to transfer more than two million otoliths collected by NOAA over the past 50 years to their new, permanent home as part of the Burke Museum’s fish collection. There they will be held safely, until the day that science finds a new way to unlock their precious data.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/03/22/fish-flight-recorders-aid-in-sustainability-efforts/jeremyincollection/\" rel=\"attachment wp-att-54277\">\u003cimg class=\"aligncenter size-full wp-image-54277\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578.jpg\" alt=\"Jeremy In Collection\" width=\"640\" height=\"427\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/03/JeremyInCollection-e1369175893578-400x267.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003c/p>\n\u003cp> \u003c/p>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Saved From Living Death: How Genetically Modifying Chestnuts Could Bring Them Back",
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"content": "\u003cfigure id=\"attachment_54812\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnut1/\" rel=\"attachment wp-att-54812\">\u003cimg class=\"size-full wp-image-54812\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnut1.jpg\" alt=\"We are getting very close to being able to bring back these gorgeous trees that used to dominate forests in the Eastern U.S. Now the big question is whether we should. Image courtesy of Wikipedia commons. \" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Chestnut1.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Chestnut1-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting very close to being able to bring back these gorgeous trees that used to dominate forests in the Eastern U.S. Now the big question is whether we should. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Castanea_dentata_large.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Around the turn of the 20th century, the forests in the eastern U.S. were dominated by the American chestnut. These “sequoia of the east” ruled the roost back then and were the cornerstone tree species. By midcentury, though, almost all of these majestic trees had been turned into shrubs.\u003c/p>\n\u003cp>No, this wasn’t magic. Instead, a fungus arrived from Asia that prevented the trees from growing bigger than this. Nowadays the only tall chestnuts are a few that happened to be planted outside of the tree’s old range. And even some of these are starting to be done in.\u003c/p>\n\u003cp>Ever since the blight started stunting the chestnut, scientists have been looking for ways to help these trees fight back. And now they may finally be getting close to a solution. Well, actually, \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/23038446\">multiple solutions\u003c/a>.\u003c/p>\n\u003cp>The one I want to focus on here is a very clever genetic modification that involves moving a wheat gene into the American chestnut. Early studies look to be very promising and these trees have even been shown to be resistant in the field. The researchers are hoping to get approval soon from the U.S. government for widespread planting.\u003c/p>\n\u003cfigure id=\"attachment_54816\" class=\"wp-caption alignright\" style=\"max-width: 265px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnutblight/\" rel=\"attachment wp-att-54816\">\u003cimg class=\"size-full wp-image-54816\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnutblight.jpg\" alt=\"These orange spots will eventually do this tree in. Just like it has with most every other American chestnut. Image courtesy of Wikimedia commons.\" width=\"265\" height=\"240\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">These orange spots will eventually do this tree in just like it has with most every other American chestnut. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Chestnut_blight_on_tree_in_Adams_County_Ohio.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>The idea behind this method rests on the knowledge that the chestnut blight needs an acidic environment to do its dirty work. The way this little monster accomplishes this is by making and then pumping oxalic acid into the tree. This is incredibly damaging to the chestnut.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>The obvious solution is to find a way to neutralize this oxalic acid. We are looking for a solution as simple as those old chemistry experiments where we neutralized hydrochloric acid with sodium hydroxide. This is where wheat can help.\u003c/p>\n\u003cp>Wheat makes an enzyme called oxalate oxidase (OxO) that breaks down oxalic acid. The researchers took the gene that has the instructions for this enzyme, the \u003cem>oxo \u003c/em>gene, and put it into the chestnut tree. The tree now makes the enzyme so that it can neutralize the blight’s oxalic acid. This approach appears to be working in making the trees more blight-resistant.\u003c/p>\n\u003cp>When researchers \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/23543108\">looked at different trees\u003c/a> that made different amounts of the enzyme, they found that only those that made a lot were resistant to the blight. In other words, there was a correlation between the amount of enzyme and resistance. When the gene was in the right place in the tree’s DNA, it could make a lot of enzyme so the tree could fight off the blight.\u003c/p>\n\u003cfigure id=\"attachment_54819\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnut2/\" rel=\"attachment wp-att-54819\">\u003cimg class=\"size-full wp-image-54819\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnut2.jpg\" alt=\"Just because we might be able to turn back time to when these trees rules, should we? Image courtesy of Wikimedia commons.\" width=\"250\" height=\"431\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Just because we might be able to turn back time to when these trees ruled, should we? Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:PSM_V84_D565_American_chestnut_mitchel_county.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>So now we have a GM tree that might restore these forests back to what they were a century or so ago. Now we have to decide whether to plant them or not.\u003c/p>\n\u003cp>This is not really an issue of the tree having been created through genetic engineering. It is very hard to come up with plausible ways that a tree with this gene could have a significant effect on the environment. The trees aren’t modified so they make their own pesticides, survive spraying by herbicides or anything like that. They simply make an enzyme from wheat that successfully battles a killer fungus by neutralizing an acid.\u003c/p>\n\u003cp>No, it has more to do with upsetting the new balance that has arisen over the last few decades in the forests back east. The forests have adjusted to the loss of the American chestnut and reintroducing the tree will only plunge the forests back into a period of readjustment. This temporary state of flux will be disruptive and so should be done for more than nostalgic reasons. There should be some environmental or economic benefit in bringing the American chestnut back.\u003c/p>\n\u003cp>Again, this discussion is not dependent on the fact that the tree is GM. The same arguments can be made for the American/Japanese/Chinese hybrids that look to be resistant too. In fact, this discussion isn’t really that different from those brought up with regards to \u003ca href=\"http://ww2.kqed.org/quest/2013/03/25/resurrection-biology-the-reality-of-bringing-back-extinct-species/\">bringing back extinct species\u003c/a>. Like those folks in Monty Python’s \u003cem>The Holy Grail\u003c/em>, the American chestnut isn’t quite dead yet, but it is close.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>So we finally have ways to bring back the American chestnut. But it may be that it took us so long to find them that we don’t need them anymore. The forests have moved on, maybe we should too.\u003c/p>\n\u003cfigure id=\"attachment_54832\" class=\"wp-caption aligncenter\" style=\"max-width: 663px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnutrange/\" rel=\"attachment wp-att-54832\">\u003cimg class=\"size-full wp-image-54832\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/ChestnutRange.jpg\" alt=\"Natural range of the American chestnut as reported in 1914. The cross hatching shows the extent of the blight back then. Image courtesy of Wikimedia commons.\" width=\"663\" height=\"600\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/ChestnutRange.jpg 663w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/ChestnutRange-400x362.jpg 400w\" sizes=\"(max-width: 663px) 100vw, 663px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Natural range of the American chestnut as reported in 1914. The cross hatching shows the extent of the blight back then. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:PSM_V84_D557_Natural_range_of_the_american_chestnut.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\n",
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"excerpt": "The American chestnut was the king of the trees in forests in the eastern U.S. until a fungus from Asia brought them down. We are getting very close to making a resistant American chestnut. Now the question is whether or not we should plant it out in the wild. ",
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"title": "Saved From Living Death: How Genetically Modifying Chestnuts Could Bring Them Back | KQED",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_54812\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnut1/\" rel=\"attachment wp-att-54812\">\u003cimg class=\"size-full wp-image-54812\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnut1.jpg\" alt=\"We are getting very close to being able to bring back these gorgeous trees that used to dominate forests in the Eastern U.S. Now the big question is whether we should. Image courtesy of Wikipedia commons. \" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Chestnut1.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Chestnut1-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting very close to being able to bring back these gorgeous trees that used to dominate forests in the Eastern U.S. Now the big question is whether we should. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Castanea_dentata_large.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>Around the turn of the 20th century, the forests in the eastern U.S. were dominated by the American chestnut. These “sequoia of the east” ruled the roost back then and were the cornerstone tree species. By midcentury, though, almost all of these majestic trees had been turned into shrubs.\u003c/p>\n\u003cp>No, this wasn’t magic. Instead, a fungus arrived from Asia that prevented the trees from growing bigger than this. Nowadays the only tall chestnuts are a few that happened to be planted outside of the tree’s old range. And even some of these are starting to be done in.\u003c/p>\n\u003cp>Ever since the blight started stunting the chestnut, scientists have been looking for ways to help these trees fight back. And now they may finally be getting close to a solution. Well, actually, \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/23038446\">multiple solutions\u003c/a>.\u003c/p>\n\u003cp>The one I want to focus on here is a very clever genetic modification that involves moving a wheat gene into the American chestnut. Early studies look to be very promising and these trees have even been shown to be resistant in the field. The researchers are hoping to get approval soon from the U.S. government for widespread planting.\u003c/p>\n\u003cfigure id=\"attachment_54816\" class=\"wp-caption alignright\" style=\"max-width: 265px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnutblight/\" rel=\"attachment wp-att-54816\">\u003cimg class=\"size-full wp-image-54816\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnutblight.jpg\" alt=\"These orange spots will eventually do this tree in. Just like it has with most every other American chestnut. Image courtesy of Wikimedia commons.\" width=\"265\" height=\"240\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">These orange spots will eventually do this tree in just like it has with most every other American chestnut. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Chestnut_blight_on_tree_in_Adams_County_Ohio.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>The idea behind this method rests on the knowledge that the chestnut blight needs an acidic environment to do its dirty work. The way this little monster accomplishes this is by making and then pumping oxalic acid into the tree. This is incredibly damaging to the chestnut.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>The obvious solution is to find a way to neutralize this oxalic acid. We are looking for a solution as simple as those old chemistry experiments where we neutralized hydrochloric acid with sodium hydroxide. This is where wheat can help.\u003c/p>\n\u003cp>Wheat makes an enzyme called oxalate oxidase (OxO) that breaks down oxalic acid. The researchers took the gene that has the instructions for this enzyme, the \u003cem>oxo \u003c/em>gene, and put it into the chestnut tree. The tree now makes the enzyme so that it can neutralize the blight’s oxalic acid. This approach appears to be working in making the trees more blight-resistant.\u003c/p>\n\u003cp>When researchers \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/23543108\">looked at different trees\u003c/a> that made different amounts of the enzyme, they found that only those that made a lot were resistant to the blight. In other words, there was a correlation between the amount of enzyme and resistance. When the gene was in the right place in the tree’s DNA, it could make a lot of enzyme so the tree could fight off the blight.\u003c/p>\n\u003cfigure id=\"attachment_54819\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnut2/\" rel=\"attachment wp-att-54819\">\u003cimg class=\"size-full wp-image-54819\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Chestnut2.jpg\" alt=\"Just because we might be able to turn back time to when these trees rules, should we? Image courtesy of Wikimedia commons.\" width=\"250\" height=\"431\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Just because we might be able to turn back time to when these trees ruled, should we? Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:PSM_V84_D565_American_chestnut_mitchel_county.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>So now we have a GM tree that might restore these forests back to what they were a century or so ago. Now we have to decide whether to plant them or not.\u003c/p>\n\u003cp>This is not really an issue of the tree having been created through genetic engineering. It is very hard to come up with plausible ways that a tree with this gene could have a significant effect on the environment. The trees aren’t modified so they make their own pesticides, survive spraying by herbicides or anything like that. They simply make an enzyme from wheat that successfully battles a killer fungus by neutralizing an acid.\u003c/p>\n\u003cp>No, it has more to do with upsetting the new balance that has arisen over the last few decades in the forests back east. The forests have adjusted to the loss of the American chestnut and reintroducing the tree will only plunge the forests back into a period of readjustment. This temporary state of flux will be disruptive and so should be done for more than nostalgic reasons. There should be some environmental or economic benefit in bringing the American chestnut back.\u003c/p>\n\u003cp>Again, this discussion is not dependent on the fact that the tree is GM. The same arguments can be made for the American/Japanese/Chinese hybrids that look to be resistant too. In fact, this discussion isn’t really that different from those brought up with regards to \u003ca href=\"http://ww2.kqed.org/quest/2013/03/25/resurrection-biology-the-reality-of-bringing-back-extinct-species/\">bringing back extinct species\u003c/a>. Like those folks in Monty Python’s \u003cem>The Holy Grail\u003c/em>, the American chestnut isn’t quite dead yet, but it is close.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>So we finally have ways to bring back the American chestnut. But it may be that it took us so long to find them that we don’t need them anymore. The forests have moved on, maybe we should too.\u003c/p>\n\u003cfigure id=\"attachment_54832\" class=\"wp-caption aligncenter\" style=\"max-width: 663px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/20/saved-from-living-death-how-genetically-modifying-chestnuts-could-bring-them-back/chestnutrange/\" rel=\"attachment wp-att-54832\">\u003cimg class=\"size-full wp-image-54832\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/ChestnutRange.jpg\" alt=\"Natural range of the American chestnut as reported in 1914. The cross hatching shows the extent of the blight back then. Image courtesy of Wikimedia commons.\" width=\"663\" height=\"600\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/ChestnutRange.jpg 663w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/ChestnutRange-400x362.jpg 400w\" sizes=\"(max-width: 663px) 100vw, 663px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Natural range of the American chestnut as reported in 1914. The cross hatching shows the extent of the blight back then. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:PSM_V84_D557_Natural_range_of_the_american_chestnut.jpg\">Wikimedia commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Next Meal: Engineering Food",
"title": "Next Meal: Engineering Food",
"headTitle": "QUEST Sustainability Science – TV series | QUEST | KQED Science",
"content": "\u003cp> \u003c/p>\n\u003cp>In this half-hour special, QUEST Northern California explores genetically engineered crops in the wake of Proposition 37, the 2012 ballot initiative that would have required foods containing genetically engineered ingredients to be labeled in California. Prop 37 lost, but some 6 million Californians voted in favor of labeling, signaling that many aren't completely comfortable with genetically engineered food.\u003c/p>\n\u003cp>Are the benefits of genetically engineered foods worth the risks?\u003c/p>\n\u003cp>\u003cstrong>Next Meal: Engineering Food\u003c/strong> explores how genetically engineered crops are made, their pros and cons, and what the future holds for research and regulations such as labeling.\u003c/p>\n\u003ch2>Ever wondered what genetically engineered crops and other foods are in the pipeline?\u003c/h2>\n\u003cp>Click through the map below and find out what's in your next meal... or in the forest on your next camping trip.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>For a bigger version of this map, click on the link below.\u003c/p>\n\u003cp>[googlemaps https://maps.google.com/maps/ms?msa=0&msid=211580250479282103391.0004da1d4aa08ab1a467c&hl=en&ie=UTF8&t=m&ll=41.244772,-18.28125&spn=90.563657,225&z=2&output=embed&w=640&h=360]\u003cbr>\nView \u003ca href=\"https://maps.google.com/maps/ms?msa=0&msid=211580250479282103391.0004da1d4aa08ab1a467c&hl=en&ie=UTF8&t=m&ll=41.244772,-18.28125&spn=90.563657,225&z=2&source=embed\">Genetically Engineered Foods in the Pipeline\u003c/a> in a larger map\u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Conventional plant breeding vs. genetic engineering – 5 differences:\u003c/h2>\n\u003cp> \u003c/p>\n\u003ch3>1. When did we start using each technique?\u003c/h3>\n\u003cp>Plant breeding is some 10,000 years old – as old as agriculture itself.\u003c/p>\n\u003cp>“The ancestors of tomatoes were the size of my thumb and they tasted very bad,” said \u003ca title=\"Eduardo Blumwald's lab at UC Davis\" href=\"http://blumwald.ucdavis.edu/\" target=\"_blank\">Eduardo Blumwald\u003c/a>, plant biologist at the University of California at Davis. “And breeding gave us what we have right now.”\u003c/p>\n\u003cfigure id=\"attachment_54133\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Tomato-paste.jpg\">\u003cimg class=\"size-thumbnail wp-image-54133\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Tomato-paste-300x169.jpg\" alt=\"Tomato paste made from genetically engineered tomatoes in the mid-1990s.\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">In the mid-1990s, tomatoes genetically engineered in California were made into a tomato paste that sold well in England. But the tomatoes were short-lived. Photo: Alan McHughen.\u003c/figcaption>\u003c/figure>\n\u003cp>The first genetically engineered food to be commercialized, the Flavr Savr tomato, was sold by Calgene, a Davis company, starting in 1994. The tomato was engineered to stay firm on the vine for longer, but it was short-lived.\u003c/p>\n\u003cp>Monsanto, the Missouri-based seed company, started selling genetically engineered soybeans and cotton in 1996. The soybeans tolerate the herbicide Roundup, so that farmers can spray it on weeds without hurting their crop in the process. The cotton keeps away pests like the bollworm.\u003c/p>\n\u003ch3>2. How do these two techniques work?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>“Classical plant breeding involves taking the female eggs from one plant and bringing them together with the male parts of another plant,” said \u003ca title=\"Peggy Lemaux, UC Berkeley\" href=\"http://pmb.berkeley.edu/profile/plemaux\" target=\"_blank\">Peggy Lemaux\u003c/a>, plant biologist at the University of California at Berkeley. “And then all that genetic information gets mixed up. Half of the information in the progeny – or children – of that cross comes from the mother and half comes from the father. And it just all gets mixed up.”\u003c/p>\n\u003cp>Depending on the plant, breeders use different strategies to cross them. Corn breeders, for example, gather pollen from female plants and shake it onto male plants. \u003ca title=\"Cucumber breeding\" href=\"http://www.youtube.com/watch?v=V5a-coN2Xgg&list=UUqyLv50NSDw9MHhtZ3OBrBw&index=8\" target=\"_blank\">Plants such as cucumbers\u003c/a> usually contain both female and male flowers on each plant. Breeders remove the male part from one flower and attach it to a female flower.\u003c/p>\n\u003cfigure id=\"attachment_54129\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Gene-gun.jpg\">\u003cimg class=\"size-thumbnail wp-image-54129\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Gene-gun-300x169.jpg\" alt='\"Gene gun\" at the University of California-Berkeley' width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Plant biologist Peggy Lemaux, at the University of California-Berkeley, uses a \"gene gun\" to genetically engineer crops like corn.\u003c/figcaption>\u003c/figure>\n\u003cp>In contrast with breeding, genetic engineering involves only one or a few genes.\u003c/p>\n\u003cp>“With genetic engineering, it’s just moving very small parts of the genetic information. You might take it out of one plant and move it into another plant,” said Lemaux.\u003c/p>\n\u003cp>In genetic engineering, genes can be transported into a plant by a type of soil bacterium. Or they can be injected into a plant using a tool called a gene gun.\u003c/p>\n\u003ch3>3. What can you do with each one?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Classical plant breeding allows scientists to do things like breed disease resistance or a higher-protein content into crops like wheat, said \u003ca title=\"UC Davis Wheat Breeding Program\" href=\"http://www.plantsciences.ucdavis.edu/dubcovsky/Breeding/WheatBreedingUCD.htm\" target=\"_blank\">Jorge Dubcovsky\u003c/a>, leader of the wheat breeding program at the University of California at Davis.\u003c/p>\n\u003cp>But when they’re breeding, scientists have to cross plants that are closely related to each other.\u003c/p>\n\u003cp>“Classical breeding is done between closely related plants, so you might take a wild variety of rice, for example, and you could cross that with modern cultivated rice,” said Peggy Lemaux. “However, maybe there are traits that you want, that you can’t find in a wild variety of rice. Maybe you want to introduce some vitamin or mineral, and you can’t find a wild rice species that would give you that particular trait. So what you have to do is you have to go and find some other organism that does make, let’s say, vitamin A, and you can pull that information out from that plant and put it in.”\u003c/p>\n\u003cp>In that scenario, genetic engineering would be required. Engineering would also be required to tweak a gene in such a way that it produces more or less of a desired trait.\u003c/p>\n\u003ch3>4. Is conventional plant breeding low-tech, while genetic engineering is high-tech?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Genetic engineering can be more expensive than conventional plant breeding, and is usually faster. But this doesn’t mean that breeding is as low-tech as you might think. In the past 15 years or so, plant breeders have been able to speed up the crossing process by using \u003ca title=\"Marker Assisted Selection in Wheat \" href=\"http://maswheat.ucdavis.edu/Education/animations/anim_mas.htm\" target=\"_blank\">genetic markers\u003c/a>.\u003c/p>\n\u003cp>“The markers allow me to see the genes that I have bred into a plant,” said Jorge Dubcovsky.\u003c/p>\n\u003cp>Many genes that scientists set out to breed into plants are difficult to see and expensive to find within the plant. A genetic marker is a piece of DNA that is easy to see and inexpensive to find within a plant. So scientists identify the markers that are on either side of the gene they’re trying to breed into a plant. This way, when they have crossed their plants to contain that gene, they can easily and inexpensively find out which plants contain their gene of interest by looking for the markers, rather than for the gene. Markers are like tiny flags on either side of the gene that make it visible to researchers.\u003c/p>\n\u003ch3>5. Do scientists do either one \u003cem>or \u003c/em>the other?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Usually, some researchers specialize in plant breeding and others in genetic engineering. But both types of scientists work closely to improve crops, said Eduardo Blumwald, who is genetically engineering rice to be drought-tolerant.\u003c/p>\n\u003cp>“We are placing new genes in those varieties which plant breeders have bred,” said Blumwald.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp> \u003c/p>\n\n",
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"excerpt": "Are the benefits of genetically engineered foods worth the risks? This half-hour QUEST Northern California special explores the pros and cons of genetically engineered crops, and what the future holds for research and regulations. ",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp> \u003c/p>\n\u003cp>In this half-hour special, QUEST Northern California explores genetically engineered crops in the wake of Proposition 37, the 2012 ballot initiative that would have required foods containing genetically engineered ingredients to be labeled in California. Prop 37 lost, but some 6 million Californians voted in favor of labeling, signaling that many aren't completely comfortable with genetically engineered food.\u003c/p>\n\u003cp>Are the benefits of genetically engineered foods worth the risks?\u003c/p>\n\u003cp>\u003cstrong>Next Meal: Engineering Food\u003c/strong> explores how genetically engineered crops are made, their pros and cons, and what the future holds for research and regulations such as labeling.\u003c/p>\n\u003ch2>Ever wondered what genetically engineered crops and other foods are in the pipeline?\u003c/h2>\n\u003cp>Click through the map below and find out what's in your next meal... or in the forest on your next camping trip.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>For a bigger version of this map, click on the link below.\u003c/p>\n\u003cp>\u003c/p>\u003cp>\u003ciframe\n src='https://maps.google.com/maps/ms?msa=0&msid=211580250479282103391.0004da1d4aa08ab1a467c&hl=en&ie=UTF8&t=m&ll=41.244772,-18.28125&spn=90.563657,225&z=2&output=embed&w=640&h=360'\n title='https://maps.google.com/maps/ms?msa=0&msid=211580250479282103391.0004da1d4aa08ab1a467c&hl=en&ie=UTF8&t=m&ll=41.244772,-18.28125&spn=90.563657,225&z=2&output=embed&w=640&h=360'\n width='640'\n height='360'\n scrolling='no'\n frameborder='no'>\u003c/iframe>\u003c/p>\u003cp>\u003cbr>\nView \u003ca href=\"https://maps.google.com/maps/ms?msa=0&msid=211580250479282103391.0004da1d4aa08ab1a467c&hl=en&ie=UTF8&t=m&ll=41.244772,-18.28125&spn=90.563657,225&z=2&source=embed\">Genetically Engineered Foods in the Pipeline\u003c/a> in a larger map\u003c/p>\n\u003cp> \u003c/p>\n\u003ch2>Conventional plant breeding vs. genetic engineering – 5 differences:\u003c/h2>\n\u003cp> \u003c/p>\n\u003ch3>1. When did we start using each technique?\u003c/h3>\n\u003cp>Plant breeding is some 10,000 years old – as old as agriculture itself.\u003c/p>\n\u003cp>“The ancestors of tomatoes were the size of my thumb and they tasted very bad,” said \u003ca title=\"Eduardo Blumwald's lab at UC Davis\" href=\"http://blumwald.ucdavis.edu/\" target=\"_blank\">Eduardo Blumwald\u003c/a>, plant biologist at the University of California at Davis. “And breeding gave us what we have right now.”\u003c/p>\n\u003cfigure id=\"attachment_54133\" class=\"wp-caption alignright\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Tomato-paste.jpg\">\u003cimg class=\"size-thumbnail wp-image-54133\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Tomato-paste-300x169.jpg\" alt=\"Tomato paste made from genetically engineered tomatoes in the mid-1990s.\" width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">In the mid-1990s, tomatoes genetically engineered in California were made into a tomato paste that sold well in England. But the tomatoes were short-lived. Photo: Alan McHughen.\u003c/figcaption>\u003c/figure>\n\u003cp>The first genetically engineered food to be commercialized, the Flavr Savr tomato, was sold by Calgene, a Davis company, starting in 1994. The tomato was engineered to stay firm on the vine for longer, but it was short-lived.\u003c/p>\n\u003cp>Monsanto, the Missouri-based seed company, started selling genetically engineered soybeans and cotton in 1996. The soybeans tolerate the herbicide Roundup, so that farmers can spray it on weeds without hurting their crop in the process. The cotton keeps away pests like the bollworm.\u003c/p>\n\u003ch3>2. How do these two techniques work?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>“Classical plant breeding involves taking the female eggs from one plant and bringing them together with the male parts of another plant,” said \u003ca title=\"Peggy Lemaux, UC Berkeley\" href=\"http://pmb.berkeley.edu/profile/plemaux\" target=\"_blank\">Peggy Lemaux\u003c/a>, plant biologist at the University of California at Berkeley. “And then all that genetic information gets mixed up. Half of the information in the progeny – or children – of that cross comes from the mother and half comes from the father. And it just all gets mixed up.”\u003c/p>\n\u003cp>Depending on the plant, breeders use different strategies to cross them. Corn breeders, for example, gather pollen from female plants and shake it onto male plants. \u003ca title=\"Cucumber breeding\" href=\"http://www.youtube.com/watch?v=V5a-coN2Xgg&list=UUqyLv50NSDw9MHhtZ3OBrBw&index=8\" target=\"_blank\">Plants such as cucumbers\u003c/a> usually contain both female and male flowers on each plant. Breeders remove the male part from one flower and attach it to a female flower.\u003c/p>\n\u003cfigure id=\"attachment_54129\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Gene-gun.jpg\">\u003cimg class=\"size-thumbnail wp-image-54129\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Gene-gun-300x169.jpg\" alt='\"Gene gun\" at the University of California-Berkeley' width=\"300\" height=\"169\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Plant biologist Peggy Lemaux, at the University of California-Berkeley, uses a \"gene gun\" to genetically engineer crops like corn.\u003c/figcaption>\u003c/figure>\n\u003cp>In contrast with breeding, genetic engineering involves only one or a few genes.\u003c/p>\n\u003cp>“With genetic engineering, it’s just moving very small parts of the genetic information. You might take it out of one plant and move it into another plant,” said Lemaux.\u003c/p>\n\u003cp>In genetic engineering, genes can be transported into a plant by a type of soil bacterium. Or they can be injected into a plant using a tool called a gene gun.\u003c/p>\n\u003ch3>3. What can you do with each one?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Classical plant breeding allows scientists to do things like breed disease resistance or a higher-protein content into crops like wheat, said \u003ca title=\"UC Davis Wheat Breeding Program\" href=\"http://www.plantsciences.ucdavis.edu/dubcovsky/Breeding/WheatBreedingUCD.htm\" target=\"_blank\">Jorge Dubcovsky\u003c/a>, leader of the wheat breeding program at the University of California at Davis.\u003c/p>\n\u003cp>But when they’re breeding, scientists have to cross plants that are closely related to each other.\u003c/p>\n\u003cp>“Classical breeding is done between closely related plants, so you might take a wild variety of rice, for example, and you could cross that with modern cultivated rice,” said Peggy Lemaux. “However, maybe there are traits that you want, that you can’t find in a wild variety of rice. Maybe you want to introduce some vitamin or mineral, and you can’t find a wild rice species that would give you that particular trait. So what you have to do is you have to go and find some other organism that does make, let’s say, vitamin A, and you can pull that information out from that plant and put it in.”\u003c/p>\n\u003cp>In that scenario, genetic engineering would be required. Engineering would also be required to tweak a gene in such a way that it produces more or less of a desired trait.\u003c/p>\n\u003ch3>4. Is conventional plant breeding low-tech, while genetic engineering is high-tech?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Genetic engineering can be more expensive than conventional plant breeding, and is usually faster. But this doesn’t mean that breeding is as low-tech as you might think. In the past 15 years or so, plant breeders have been able to speed up the crossing process by using \u003ca title=\"Marker Assisted Selection in Wheat \" href=\"http://maswheat.ucdavis.edu/Education/animations/anim_mas.htm\" target=\"_blank\">genetic markers\u003c/a>.\u003c/p>\n\u003cp>“The markers allow me to see the genes that I have bred into a plant,” said Jorge Dubcovsky.\u003c/p>\n\u003cp>Many genes that scientists set out to breed into plants are difficult to see and expensive to find within the plant. A genetic marker is a piece of DNA that is easy to see and inexpensive to find within a plant. So scientists identify the markers that are on either side of the gene they’re trying to breed into a plant. This way, when they have crossed their plants to contain that gene, they can easily and inexpensively find out which plants contain their gene of interest by looking for the markers, rather than for the gene. Markers are like tiny flags on either side of the gene that make it visible to researchers.\u003c/p>\n\u003ch3>5. Do scientists do either one \u003cem>or \u003c/em>the other?\u003c/h3>\n\u003cp> \u003c/p>\n\u003cp>Usually, some researchers specialize in plant breeding and others in genetic engineering. But both types of scientists work closely to improve crops, said Eduardo Blumwald, who is genetically engineering rice to be drought-tolerant.\u003c/p>\n\u003cp>“We are placing new genes in those varieties which plant breeders have bred,” said Blumwald.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"disqusTitle": "Scrounging for Research Dollars",
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"content": "\u003cfigure id=\"attachment_53735\" class=\"wp-caption aligncenter\" style=\"max-width: 639px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/06/scrounging-for-research-dollars/lab/\" rel=\"attachment wp-att-53735\">\u003cimg class=\"size-full wp-image-53735\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Lab.jpg\" alt=\"I don't have time for this, I need to get back to writing grants! Image courtesy of David Shankbone, Wikimedia Commons.\" width=\"639\" height=\"340\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Lab.jpg 639w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Lab-400x213.jpg 400w\" sizes=\"(max-width: 639px) 100vw, 639px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">I don't have time for this, I need to get back to writing grants! Image courtesy of David Shankbone, Wikimedia Commons.\u003c/figcaption>\u003c/figure>\n\u003cp>If you’re a scientist these days, getting the money to do your research is a lot like getting into Stanford or Yale. Assuming you aren’t rich or connected, being incredibly skilled, hardworking and accomplished isn’t enough. You need to get lucky too.\u003c/p>\n\u003cp>The big difference is that in terms of funding for research, there aren’t really any back up schools. If you don’t get into your Ivy League college, you don’t get your college degree. The best you can do is scrape together a few part-time jobs to stay in business so you can apply over and over again to the same school. No wonder so many scientists are becoming discouraged.\u003c/p>\n\u003cp>For those of you who don’t know how scientists at universities get their money, here is a quick, crash course. First off, scientists aren’t paid by a university to do their research. They are expected to raise that money on their own. They are given a bit of money to get started, but the university supplies almost no money after that. In fact, they take a good chunk of the money you manage to raise for overhead costs (buildings, electricity, name recognition, etc.).\u003c/p>\n\u003cp>This didn’t used to be a big deal. Yes, it was an inconvenience but there was enough money so that if you had a good idea and some data to support it, you had a pretty good shot at getting funded. This is no longer true.\u003c/p>\n\u003cp>These days most higher-level scientists are spending less and less time doing science and more and more time writing grants to try to get research funded. If they don’t have a big name and/or come from a big school, odds are most if not all of the grants won’t be funded. And even if they have the reputation and come from what is deemed to be a big school, they still may end up penniless.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Someone I know at Stanford summarized his situation like this:\u003c/p>\n\u003cp>\u003cem>This year I'll be submitting six RO1 grants, each of which take about a month's worth of effort. Given that the current funding levels are less than 10%, I'll be lucky if one gets funded so I can keep doing my research. Three of these proposals are seeking funding to continue existing research projects that serve the scientific community; if they aren’t funded, those projects will stop.\u003c/em>\u003c/p>\n\u003cp>As you can tell, he is writing as fast as he can to try to keep at least some of his projects going. He is not doing much research on his own, he is just trying to get enough money so the graduate students and other people in his lab can do some science. Not what he was trained for!\u003c/p>\n\u003cp>Not only that, but as he says, some of his ongoing projects will lose their funding. This isn’t because they aren’t worthy. Instead they won’t be funded because they didn’t get the lucky six numbers to win the lottery this round.\u003c/p>\n\u003cfigure id=\"attachment_53738\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/06/scrounging-for-research-dollars/obamanas/\" rel=\"attachment wp-att-53738\">\u003cimg class=\"size-full wp-image-53738\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/ObamaNAS.jpg\" alt=\"President Obama recognizes the problems with science funding. \" width=\"250\" height=\"230\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">President Obama recognizes the problems with science funding.\u003c/figcaption>\u003c/figure>\n\u003cp>Chaotic funding like this slows research down as ideas are not allowed to flower but instead die or go dormant. And even if they are picked up again, research is slowed as the new group has to learn the subtleties of that particular project. This is no way to run a business!\u003c/p>\n\u003cp>At least some people in government are recognizing this reality. President Obama in a \u003ca href=\"http://www.bizjournals.com/twincities/news/2013/04/29/obama-sequester-could-cost-us-up-to.html\">speech \u003c/a>to the National Academy of Sciences suggested that sequestration could cost two years of research. And this is just the sequestration; it doesn’t include the lost years from the drop off in funding that has already happened in the last few years.\u003c/p>\n\u003cp>As you might expect, this isn’t just a U.S. problem. A recent \u003ca href=\"http://www.guardian.co.uk/science/occams-corner/2013/apr/02/1?CMP=twt_fd\">article \u003c/a>in the Guardian points out that the same sorts of things are happening in Europe and Australia too.\u003c/p>\n\u003cp>In a time of decreased funding, we have to decide if having fewer scientists able to do research is OK. If it is, then we can keep the same system in place and have scientists writing grant after grant, trying to raise money for their research. Hopefully the best grant writers are also the best scientists.\u003c/p>\n\u003cp>If we want more scientists able to do research, then we have to decide what to do. One idea might be to streamline the granting process to save money so that more grants are funded. The occasional stinker of a project might slip through, but that might be OK if many more grants can be funded. Another idea would be more money for research, but you can’t squeeze blood from a turnip. There simply may not be the money to fund research under the current system so that a scientist has a reasonable chance at getting funded.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The worst part is we have to count on Congress to try to deal with this. I suspect things will go on like they have been for a very long time.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_53735\" class=\"wp-caption aligncenter\" style=\"max-width: 639px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/06/scrounging-for-research-dollars/lab/\" rel=\"attachment wp-att-53735\">\u003cimg class=\"size-full wp-image-53735\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Lab.jpg\" alt=\"I don't have time for this, I need to get back to writing grants! Image courtesy of David Shankbone, Wikimedia Commons.\" width=\"639\" height=\"340\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Lab.jpg 639w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Lab-400x213.jpg 400w\" sizes=\"(max-width: 639px) 100vw, 639px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">I don't have time for this, I need to get back to writing grants! Image courtesy of David Shankbone, Wikimedia Commons.\u003c/figcaption>\u003c/figure>\n\u003cp>If you’re a scientist these days, getting the money to do your research is a lot like getting into Stanford or Yale. Assuming you aren’t rich or connected, being incredibly skilled, hardworking and accomplished isn’t enough. You need to get lucky too.\u003c/p>\n\u003cp>The big difference is that in terms of funding for research, there aren’t really any back up schools. If you don’t get into your Ivy League college, you don’t get your college degree. The best you can do is scrape together a few part-time jobs to stay in business so you can apply over and over again to the same school. No wonder so many scientists are becoming discouraged.\u003c/p>\n\u003cp>For those of you who don’t know how scientists at universities get their money, here is a quick, crash course. First off, scientists aren’t paid by a university to do their research. They are expected to raise that money on their own. They are given a bit of money to get started, but the university supplies almost no money after that. In fact, they take a good chunk of the money you manage to raise for overhead costs (buildings, electricity, name recognition, etc.).\u003c/p>\n\u003cp>This didn’t used to be a big deal. Yes, it was an inconvenience but there was enough money so that if you had a good idea and some data to support it, you had a pretty good shot at getting funded. This is no longer true.\u003c/p>\n\u003cp>These days most higher-level scientists are spending less and less time doing science and more and more time writing grants to try to get research funded. If they don’t have a big name and/or come from a big school, odds are most if not all of the grants won’t be funded. And even if they have the reputation and come from what is deemed to be a big school, they still may end up penniless.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Someone I know at Stanford summarized his situation like this:\u003c/p>\n\u003cp>\u003cem>This year I'll be submitting six RO1 grants, each of which take about a month's worth of effort. Given that the current funding levels are less than 10%, I'll be lucky if one gets funded so I can keep doing my research. Three of these proposals are seeking funding to continue existing research projects that serve the scientific community; if they aren’t funded, those projects will stop.\u003c/em>\u003c/p>\n\u003cp>As you can tell, he is writing as fast as he can to try to keep at least some of his projects going. He is not doing much research on his own, he is just trying to get enough money so the graduate students and other people in his lab can do some science. Not what he was trained for!\u003c/p>\n\u003cp>Not only that, but as he says, some of his ongoing projects will lose their funding. This isn’t because they aren’t worthy. Instead they won’t be funded because they didn’t get the lucky six numbers to win the lottery this round.\u003c/p>\n\u003cfigure id=\"attachment_53738\" class=\"wp-caption alignright\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/06/scrounging-for-research-dollars/obamanas/\" rel=\"attachment wp-att-53738\">\u003cimg class=\"size-full wp-image-53738\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/ObamaNAS.jpg\" alt=\"President Obama recognizes the problems with science funding. \" width=\"250\" height=\"230\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">President Obama recognizes the problems with science funding.\u003c/figcaption>\u003c/figure>\n\u003cp>Chaotic funding like this slows research down as ideas are not allowed to flower but instead die or go dormant. And even if they are picked up again, research is slowed as the new group has to learn the subtleties of that particular project. This is no way to run a business!\u003c/p>\n\u003cp>At least some people in government are recognizing this reality. President Obama in a \u003ca href=\"http://www.bizjournals.com/twincities/news/2013/04/29/obama-sequester-could-cost-us-up-to.html\">speech \u003c/a>to the National Academy of Sciences suggested that sequestration could cost two years of research. And this is just the sequestration; it doesn’t include the lost years from the drop off in funding that has already happened in the last few years.\u003c/p>\n\u003cp>As you might expect, this isn’t just a U.S. problem. A recent \u003ca href=\"http://www.guardian.co.uk/science/occams-corner/2013/apr/02/1?CMP=twt_fd\">article \u003c/a>in the Guardian points out that the same sorts of things are happening in Europe and Australia too.\u003c/p>\n\u003cp>In a time of decreased funding, we have to decide if having fewer scientists able to do research is OK. If it is, then we can keep the same system in place and have scientists writing grant after grant, trying to raise money for their research. Hopefully the best grant writers are also the best scientists.\u003c/p>\n\u003cp>If we want more scientists able to do research, then we have to decide what to do. One idea might be to streamline the granting process to save money so that more grants are funded. The occasional stinker of a project might slip through, but that might be OK if many more grants can be funded. Another idea would be more money for research, but you can’t squeeze blood from a turnip. There simply may not be the money to fund research under the current system so that a scientist has a reasonable chance at getting funded.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The worst part is we have to count on Congress to try to deal with this. I suspect things will go on like they have been for a very long time.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>\u003cstrong>A vast and teeming crew\u003c/strong>\u003c/p>\n\u003cp>Here's something to stop and consider: You are mostly not you.\u003c/p>\n\u003cp>Ninety percent of the cells in your body don't have your DNA. They weren't in you when you were in the womb. Instead, they belong to trillions of tiny bacteria and other microbes that live in your stomach, your mouth and on your skin, among other places. Collectively, they make up between five and ten pounds of your body weight, a vast and teeming crew known as the microbiome.\u003c/p>\n\u003cp>Scientists have known about the microbiome for some time, but the advent of relatively inexpensive DNA sequencing has transformed the research, making it possible to sequence – and therefore identify – thousands of species of bacteria and other microbes at once.\u003c/p>\n\u003caside class=\"alignright\">\u003cstrong>The Human Microbiome: A Rogue's Gallery\u003c/strong>\n\u003cfigure id=\"attachment_53922\" class=\"wp-caption aligncenter\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/\">\u003cimg class=\"size-full wp-image-53922\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/rogues.jpg\" alt=\"rogues\" width=\"320\" height=\"217\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">What are these creatures living inside us? Find out here.\u003c/figcaption>\u003c/figure>\n\u003c/aside>\n\u003cp>Among those doing the cataloging is Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Not long ago, Pollard was chatting with a few colleagues in a weekly meeting when one of them, a grad student named Chris Gignoux, mentioned some field work he'd been doing in a remote part of South Africa with an indigenous sheep and goat herding group called the Khoisan.\u003c/p>\n\u003cp>The Khiosan are thought to be the oldest genetic group on earth, ancestors of the rest of us. Even their language is unique, a \u003ca href=\"http://www.youtube.com/watch?v=c246fZ-7z1w\">“click” language\u003c/a> with consonants found nowhere else in the world.\u003c/p>\n\u003cp>Gignoux is part of a team trying to \u003ca href=\"http://www.nature.com/ncomms/journal/v3/n10/fig_tab/ncomms2140_F2.html\">piece together\u003c/a> the Khoisan's evolutionary history by studying their DNA, which the team extracts from saliva samples collected during field research trips to South Africa.\u003c/p>\n\u003cp>But the scientists were running into a problem. The Khoisan samples were contaminated with non-human cells: bacteria and other microbes that live in the Khoisan's mouths.\u003c/p>\n\u003cp>“The exact DNA that they were viewing as contamination was very interesting to us,” says Pollard.\u003c/p>\n\u003cp>\u003cstrong> A garden in your gut\u003c/strong>\u003c/p>\n\u003caside class=\"pullquote alignleft\">\"The exact DNA that they were viewing as contamination was very interesting to us,” says Pollard.\u003c/aside>\n\u003cp>In recent years, scientists have come to see these bacteria and other microbes as a delicate ecosystem inside each of us. You can think of it as a garden in your guts, one you are constantly tending and adding to every time you eat a meal or are exposed to something in your environment.\u003c/p>\n\u003cp>And just like a garden, things can get out of whack. Invasive species take over; certain plants die off.\u003c/p>\n\u003cp>And when this happens, scientists believe, people can get sick.\u003c/p>\n\u003cp>Michael Fischbach is an assistant professor in the school of pharmacy at UCSF. He reels off a list of diseases that might – repeat, \u003cem>might\u003c/em> -- be connected to changes in our microbiome: “the inflammatory bowel diseases, including Crohn's disease. Possibly diabetes and obesity. Possibly even allergic diseases like asthma.”\u003c/p>\n\u003cp>This is new science. No one really knows. But Fischbach and others who study the microbiome are excited about the potential here, in part because of two recent discoveries.\u003c/p>\n\u003cfigure id=\"attachment_53921\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/pollard.jpg\" alt=\"Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco, is working on cataloging the human microbiome. (Courtesy photo)\" width=\"640\" height=\"485\">\u003cfigcaption class=\"wp-caption-text\">Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco, is working on cataloging the human microbiome. (Courtesy photo)\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Fecal transplants and an unlikely connection\u003cbr>\n\u003c/strong>\u003c/p>\n\u003cp>One was the announcement last year that people suffering from a stubborn bacterial infection called C.difficile were cured after receiving \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365524/\">fecal transplants\u003c/a>. They ingested fresh feces – collected from healthy donors and teeming with healthy bacteria – through a tube in their nose. It was a microbiome transplant, and it worked.\u003c/p>\n\u003cp>The second development came last month, when a researcher at the Cleveland Clinic published \u003ca href=\"http://my.clevelandclinic.org/media_relations/library/2013/2013-04-07-cleveland-clinic-researchers-discover-link-between-heart-disease-and-compound-found-in-red-meat-energy-drinks.aspx\">results\u003c/a> connecting bacteria in people's guts to heart disease.\u003c/p>\n\u003cp>“Nobody would have put heart disease on that list,” says Fischbach.\u003c/p>\n\u003cp>He says the announcement sent ripples of optimism throughout the microbiome research community. “The notion that you could come up with something that is going to surprise even those who have been working on it for some time is very much in the air.”\u003c/p>\n\u003cp>Also fueling the excitement is the recent completion of the \u003ca href=\"http://commonfund.nih.gov/hmp/\">Human Microbiome Project\u003c/a>, an effort, funded by the National Institutes of Health, to identify and catalogue the microbiota of 242 healthy American volunteers.\u003c/p>\n\u003cp>Now that scientists are starting to get a handle on what kinds of microbes live in the human body and, roughly, how those populations differ from one individual to another, a key question will be whether there is such a thing as an “ideal” microbiome.\u003c/p>\n\u003cp>In other words, if a bad, or imbalanced microbiome can make people sick, what does a good, balanced microbiome look like? What are the microbes that have evolved to keep us healthy, and how do they do it?\u003cbr>\n\u003cstrong>\u003cbr>\nWas there a microbial Garden of Eden?\u003c/strong>\u003c/p>\n\u003cp>This is a hard question to answer because most of us have made huge, sweeping changes to our microbiomes at least several times in our lives by taking antibiotics.\u003c/p>\n\u003cp>David Relman, a professor of medicine at Stanford, was one of the first scientists to use DNA sequencing to study the makeup of the microbiome, using a swab from the inside of his own cheek.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Antibiotics are \"more like a cluster bomb,\" says Relman. \"They're indiscriminate. And there's a lot of collateral damage.”\u003c/aside>\n\u003cp>Since then, his work has explored how antibiotics affect the microbiome, and how long those \u003ca href=\"http://www.pnas.org/content/early/2010/09/14/1000087107\">changes persist\u003c/a>. He says while antibiotics have saved millions of lives, they’re a blunt instrument.\u003c/p>\n\u003cp>“In the past, we thought of antibiotics as magic bullets,” Relman says. “But – I hate using the military metaphor – they're more like a cluster bomb, or a neutron bomb. They're indiscriminate. And there's a lot of collateral damage.”\u003c/p>\n\u003cp>That collateral damage includes healthy bacteria, which may play important roles in digestion and other functions. Antibiotics can also create ideal environments for harmful bacteria to thrive.\u003c/p>\n\u003cp>Sometimes, the balance restores itself. Other times, the changes may be permanent. If a particular strain of bacteria is lost, it can't be passed on from one human generation to the next.\u003c/p>\n\u003cp>But this is hard to study. Because there’s almost no one out there who hasn't taken antibiotics. Which brings us back to the Khoisan.\u003c/p>\n\u003cp>\u003cstrong>Learning from the Khoisan\u003c/strong>\u003c/p>\n\u003cp>What occurred to Katie Pollard is that the Khoisan for the most part haven’t had that repeated antibiotic exposure. If researchers can find bacteria in the Khoisan that don’t show up in the saliva of industrialized groups, she says, “that would suggest that something in the modern lifestyle has potentially wiped out these bacteria.”\u003c/p>\n\u003cp>This work is just beginning. So far, Pollard's team has identified about 900 species of microbes in the Khoisan saliva. Next, they'll compare those species to samples from other populations to see whether there are any completely novel microbes in the Khoisan, microbes she and others haven't seen before.\u003c/p>\n\u003cp>Lest anyone start thinking that the Khoisan microbiome could be some sort of wholesale solution to modern ills (maybe imported through some kind of trans-Atlantic fecal transplant?) think again.\u003c/p>\n\u003cp>Among those 900 bacterial species identified, says Pollard, are several that you definitely wouldn't want, a fact that becomes clear when you look at photos of the Khoisan, many of whom are missing teeth.\u003c/p>\n\u003cp>“Many of the bacteria we've found are known pathogens,” says Pollard, “in terms of gum disease or enhancing plaque.”\u003c/p>\n\u003cp>Modern medicine has not been all bad for the microbiome.\u003c/p>\n\u003cp>Pollard and others who do DNA sequencing on gut microbes face a massive computational challenge, one that makes the human genome project look like a cakewalk.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>But the end result, say Pollard and others, could be new insights into how we could tweak, even curate the bacteria in our bodies, to make ourselves healthier.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>\u003cstrong>A vast and teeming crew\u003c/strong>\u003c/p>\n\u003cp>Here's something to stop and consider: You are mostly not you.\u003c/p>\n\u003cp>Ninety percent of the cells in your body don't have your DNA. They weren't in you when you were in the womb. Instead, they belong to trillions of tiny bacteria and other microbes that live in your stomach, your mouth and on your skin, among other places. Collectively, they make up between five and ten pounds of your body weight, a vast and teeming crew known as the microbiome.\u003c/p>\n\u003cp>Scientists have known about the microbiome for some time, but the advent of relatively inexpensive DNA sequencing has transformed the research, making it possible to sequence – and therefore identify – thousands of species of bacteria and other microbes at once.\u003c/p>\n\u003caside class=\"alignright\">\u003cstrong>The Human Microbiome: A Rogue's Gallery\u003c/strong>\n\u003cfigure id=\"attachment_53922\" class=\"wp-caption aligncenter\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/\">\u003cimg class=\"size-full wp-image-53922\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/rogues.jpg\" alt=\"rogues\" width=\"320\" height=\"217\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">What are these creatures living inside us? Find out here.\u003c/figcaption>\u003c/figure>\n\u003c/aside>\n\u003cp>Among those doing the cataloging is Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Not long ago, Pollard was chatting with a few colleagues in a weekly meeting when one of them, a grad student named Chris Gignoux, mentioned some field work he'd been doing in a remote part of South Africa with an indigenous sheep and goat herding group called the Khoisan.\u003c/p>\n\u003cp>The Khiosan are thought to be the oldest genetic group on earth, ancestors of the rest of us. Even their language is unique, a \u003ca href=\"http://www.youtube.com/watch?v=c246fZ-7z1w\">“click” language\u003c/a> with consonants found nowhere else in the world.\u003c/p>\n\u003cp>Gignoux is part of a team trying to \u003ca href=\"http://www.nature.com/ncomms/journal/v3/n10/fig_tab/ncomms2140_F2.html\">piece together\u003c/a> the Khoisan's evolutionary history by studying their DNA, which the team extracts from saliva samples collected during field research trips to South Africa.\u003c/p>\n\u003cp>But the scientists were running into a problem. The Khoisan samples were contaminated with non-human cells: bacteria and other microbes that live in the Khoisan's mouths.\u003c/p>\n\u003cp>“The exact DNA that they were viewing as contamination was very interesting to us,” says Pollard.\u003c/p>\n\u003cp>\u003cstrong> A garden in your gut\u003c/strong>\u003c/p>\n\u003caside class=\"pullquote alignleft\">\"The exact DNA that they were viewing as contamination was very interesting to us,” says Pollard.\u003c/aside>\n\u003cp>In recent years, scientists have come to see these bacteria and other microbes as a delicate ecosystem inside each of us. You can think of it as a garden in your guts, one you are constantly tending and adding to every time you eat a meal or are exposed to something in your environment.\u003c/p>\n\u003cp>And just like a garden, things can get out of whack. Invasive species take over; certain plants die off.\u003c/p>\n\u003cp>And when this happens, scientists believe, people can get sick.\u003c/p>\n\u003cp>Michael Fischbach is an assistant professor in the school of pharmacy at UCSF. He reels off a list of diseases that might – repeat, \u003cem>might\u003c/em> -- be connected to changes in our microbiome: “the inflammatory bowel diseases, including Crohn's disease. Possibly diabetes and obesity. Possibly even allergic diseases like asthma.”\u003c/p>\n\u003cp>This is new science. No one really knows. But Fischbach and others who study the microbiome are excited about the potential here, in part because of two recent discoveries.\u003c/p>\n\u003cfigure id=\"attachment_53921\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/pollard.jpg\" alt=\"Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco, is working on cataloging the human microbiome. (Courtesy photo)\" width=\"640\" height=\"485\">\u003cfigcaption class=\"wp-caption-text\">Katie Pollard, a geneticist at the Gladstone Institutes in San Francisco, is working on cataloging the human microbiome. (Courtesy photo)\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Fecal transplants and an unlikely connection\u003cbr>\n\u003c/strong>\u003c/p>\n\u003cp>One was the announcement last year that people suffering from a stubborn bacterial infection called C.difficile were cured after receiving \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365524/\">fecal transplants\u003c/a>. They ingested fresh feces – collected from healthy donors and teeming with healthy bacteria – through a tube in their nose. It was a microbiome transplant, and it worked.\u003c/p>\n\u003cp>The second development came last month, when a researcher at the Cleveland Clinic published \u003ca href=\"http://my.clevelandclinic.org/media_relations/library/2013/2013-04-07-cleveland-clinic-researchers-discover-link-between-heart-disease-and-compound-found-in-red-meat-energy-drinks.aspx\">results\u003c/a> connecting bacteria in people's guts to heart disease.\u003c/p>\n\u003cp>“Nobody would have put heart disease on that list,” says Fischbach.\u003c/p>\n\u003cp>He says the announcement sent ripples of optimism throughout the microbiome research community. “The notion that you could come up with something that is going to surprise even those who have been working on it for some time is very much in the air.”\u003c/p>\n\u003cp>Also fueling the excitement is the recent completion of the \u003ca href=\"http://commonfund.nih.gov/hmp/\">Human Microbiome Project\u003c/a>, an effort, funded by the National Institutes of Health, to identify and catalogue the microbiota of 242 healthy American volunteers.\u003c/p>\n\u003cp>Now that scientists are starting to get a handle on what kinds of microbes live in the human body and, roughly, how those populations differ from one individual to another, a key question will be whether there is such a thing as an “ideal” microbiome.\u003c/p>\n\u003cp>In other words, if a bad, or imbalanced microbiome can make people sick, what does a good, balanced microbiome look like? What are the microbes that have evolved to keep us healthy, and how do they do it?\u003cbr>\n\u003cstrong>\u003cbr>\nWas there a microbial Garden of Eden?\u003c/strong>\u003c/p>\n\u003cp>This is a hard question to answer because most of us have made huge, sweeping changes to our microbiomes at least several times in our lives by taking antibiotics.\u003c/p>\n\u003cp>David Relman, a professor of medicine at Stanford, was one of the first scientists to use DNA sequencing to study the makeup of the microbiome, using a swab from the inside of his own cheek.\u003c/p>\n\u003caside class=\"pullquote alignleft\">Antibiotics are \"more like a cluster bomb,\" says Relman. \"They're indiscriminate. And there's a lot of collateral damage.”\u003c/aside>\n\u003cp>Since then, his work has explored how antibiotics affect the microbiome, and how long those \u003ca href=\"http://www.pnas.org/content/early/2010/09/14/1000087107\">changes persist\u003c/a>. He says while antibiotics have saved millions of lives, they’re a blunt instrument.\u003c/p>\n\u003cp>“In the past, we thought of antibiotics as magic bullets,” Relman says. “But – I hate using the military metaphor – they're more like a cluster bomb, or a neutron bomb. They're indiscriminate. And there's a lot of collateral damage.”\u003c/p>\n\u003cp>That collateral damage includes healthy bacteria, which may play important roles in digestion and other functions. Antibiotics can also create ideal environments for harmful bacteria to thrive.\u003c/p>\n\u003cp>Sometimes, the balance restores itself. Other times, the changes may be permanent. If a particular strain of bacteria is lost, it can't be passed on from one human generation to the next.\u003c/p>\n\u003cp>But this is hard to study. Because there’s almost no one out there who hasn't taken antibiotics. Which brings us back to the Khoisan.\u003c/p>\n\u003cp>\u003cstrong>Learning from the Khoisan\u003c/strong>\u003c/p>\n\u003cp>What occurred to Katie Pollard is that the Khoisan for the most part haven’t had that repeated antibiotic exposure. If researchers can find bacteria in the Khoisan that don’t show up in the saliva of industrialized groups, she says, “that would suggest that something in the modern lifestyle has potentially wiped out these bacteria.”\u003c/p>\n\u003cp>This work is just beginning. So far, Pollard's team has identified about 900 species of microbes in the Khoisan saliva. Next, they'll compare those species to samples from other populations to see whether there are any completely novel microbes in the Khoisan, microbes she and others haven't seen before.\u003c/p>\n\u003cp>Lest anyone start thinking that the Khoisan microbiome could be some sort of wholesale solution to modern ills (maybe imported through some kind of trans-Atlantic fecal transplant?) think again.\u003c/p>\n\u003cp>Among those 900 bacterial species identified, says Pollard, are several that you definitely wouldn't want, a fact that becomes clear when you look at photos of the Khoisan, many of whom are missing teeth.\u003c/p>\n\u003cp>“Many of the bacteria we've found are known pathogens,” says Pollard, “in terms of gum disease or enhancing plaque.”\u003c/p>\n\u003cp>Modern medicine has not been all bad for the microbiome.\u003c/p>\n\u003cp>Pollard and others who do DNA sequencing on gut microbes face a massive computational challenge, one that makes the human genome project look like a cakewalk.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>But the end result, say Pollard and others, could be new insights into how we could tweak, even curate the bacteria in our bodies, to make ourselves healthier.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>Scientists are starting to get a handle on what kinds of microbes live in the human body and, roughly, how those populations differ from one individual to another. A key question now is whether there is such a thing as an “ideal” microbiome. In the meantime, get to know some of the microbes that may be in your gut. \u003c/p>\n\u003cfigure id=\"attachment_53890\" class=\"wp-caption alignleft\" style=\"max-width: 600px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/empylori/\" rel=\"attachment wp-att-53890\">\u003cimg class=\"size-full wp-image-53890\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/EMpylori.jpg\" alt=\"H. pylori has lived in our stomachs for 200,000 years. (Photo: Yutaka Tsutsumi)\" width=\"600\" height=\"400\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/EMpylori.jpg 600w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/EMpylori-400x267.jpg 400w\" sizes=\"(max-width: 600px) 100vw, 600px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003cem>H. pylori\u003c/em> has lived in our stomachs for 200,000 years. (Photo: Dr. Yutaka Tsutsumi)\u003c/figcaption>\u003c/figure>\n\u003cp dir=\"ltr\">\u003cstrong>\u003cem>Helicobacter pylori\u003c/em>\u003c/strong>\u003c/p>\n\u003cp>Humans have a love-hate relationship with \u003cem>H. pylori\u003c/em>. It has dwelled inside our stomachs for 200,000 or so years, but its role is unclear. Scientists believe the microbe causes peptic ulcers and have linked it with an increased risk of stomach cancer. But the percentage of people with \u003cem>H. pylori\u003c/em> has been shrinking, particularly in the Western world where antibiotic use has been widespread for more than half a century. Those lacking in \u003cem>H. pylori\u003c/em> may be at higher risk for asthma or obesity, since the bacteria helps tell us when we’re full. Scientists aren’t sure whether the absence of the microbe actually causes asthma or obesity, but the two occurrences do correlate.\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.newyorker.com/reporting/2012/10/22/121022fa_fact_specter\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_53889\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/clostridium_difficile_01/\" rel=\"attachment wp-att-53889\">\u003cimg class=\"size-full wp-image-53889\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Clostridium_difficile_01.png\" alt='C. difficile can cause some nasty problems if left unchecked by \"good\" bacteria. (Photo: Centers for Disease Control)' width=\"320\" height=\"auto\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Clostridium_difficile_01.png 447w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Clostridium_difficile_01-400x268.png 400w\" sizes=\"(max-width: 447px) 100vw, 447px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">C. difficile can cause some nasty problems if left unchecked by \"good\" bacteria. (Photo: Centers for Disease Control)\u003c/figcaption>\u003c/figure>\n\u003cdiv>\u003cstrong>\u003cem>Clostridium difficile\u003c/em>\u003c/strong>\u003c/div>\n\u003cp>The “good” bacteria in your gut often keep bad stuff at bay. When the good guys are destroyed (possibly with antibiotics), \u003cem>C. difficile\u003c/em> takes over, which can cause severe diarrhea or deadly inflammation of the colon. The condition most commonly affects hospitalized older adults or those in long-term care. The cure: more antibiotics — or a fecal transplant.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.mayoclinic.com/health/c-difficile/DS00736\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003cstrong>Bifidobacterium\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_53888\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/bifidobacterium/\" rel=\"attachment wp-att-53888\">\u003cimg class=\"size-full wp-image-53888\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Bifidobacterium.jpg\" alt=\"Bifidobacterium lives throughout the body and can be damaged by antibiotic treatments. (Photo: Wikimedia Commons)\" width=\"320\" height=\"auto\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Bifidobacterium lives throughout the body and can be damaged by antibiotic treatments. (Photo: Wikimedia Commons)\u003c/figcaption>\u003c/figure>\n\u003cp dir=\"ltr\">The gut biota ecosystem is a dramatically changing environment in the first two years of life. Bifidobacterium include a range of bacteria species that exist symbiotically throughout our bodies. But the evolution of Bifidobacterium in infant bodies can be stunted by early antibiotic treatment. The bacteria are linked with many probiotic benefits, and scientists do not yet understand the long-term health consequences of reducing their numbers.\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/22948872\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_53891\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/p-ging/\" rel=\"attachment wp-att-53891\">\u003cimg class=\"size-full wp-image-53891\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/p-ging.jpg\" alt=\"P. gingivalis can make your teeth fall out. (Photo: Flickr user AJC1)\" width=\"320\" height=\"auto\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">P. gingivalis can make your teeth fall out. (Photo: Flickr user AJC1)\u003c/figcaption>\u003c/figure>\n\u003cp> \u003c/p>\n\u003cp>\u003cstrong>\u003cem>Porphyromonas gingivalis\u003c/em>\u003c/strong>\u003c/p>\n\u003cp>Did you brush your teeth this morning? The microflora in our mouths can cause some real problems. Take \u003cem>P. gingivalis\u003c/em> (pictured). The bacteria places a role in the onset of periodontitis, an inflammation of the gums that causes teeth to fall out. \u003cem>P. gingivalis\u003c/em> is also associated with rheumatoid arthritis and heart disease. It’s less abundant in the mouth than, say, \u003cem>Streptococcus parasanguinis\u003c/em>. Those bacteria colonize the surface of your teeth, forming plaque.\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003c/p>\n\u003cp> \u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>Scientists are starting to get a handle on what kinds of microbes live in the human body and, roughly, how those populations differ from one individual to another. A key question now is whether there is such a thing as an “ideal” microbiome. In the meantime, get to know some of the microbes that may be in your gut. \u003c/p>\n\u003cfigure id=\"attachment_53890\" class=\"wp-caption alignleft\" style=\"max-width: 600px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/empylori/\" rel=\"attachment wp-att-53890\">\u003cimg class=\"size-full wp-image-53890\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/EMpylori.jpg\" alt=\"H. pylori has lived in our stomachs for 200,000 years. (Photo: Yutaka Tsutsumi)\" width=\"600\" height=\"400\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/EMpylori.jpg 600w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/EMpylori-400x267.jpg 400w\" sizes=\"(max-width: 600px) 100vw, 600px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">\u003cem>H. pylori\u003c/em> has lived in our stomachs for 200,000 years. (Photo: Dr. Yutaka Tsutsumi)\u003c/figcaption>\u003c/figure>\n\u003cp dir=\"ltr\">\u003cstrong>\u003cem>Helicobacter pylori\u003c/em>\u003c/strong>\u003c/p>\n\u003cp>Humans have a love-hate relationship with \u003cem>H. pylori\u003c/em>. It has dwelled inside our stomachs for 200,000 or so years, but its role is unclear. Scientists believe the microbe causes peptic ulcers and have linked it with an increased risk of stomach cancer. But the percentage of people with \u003cem>H. pylori\u003c/em> has been shrinking, particularly in the Western world where antibiotic use has been widespread for more than half a century. Those lacking in \u003cem>H. pylori\u003c/em> may be at higher risk for asthma or obesity, since the bacteria helps tell us when we’re full. Scientists aren’t sure whether the absence of the microbe actually causes asthma or obesity, but the two occurrences do correlate.\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.newyorker.com/reporting/2012/10/22/121022fa_fact_specter\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_53889\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/clostridium_difficile_01/\" rel=\"attachment wp-att-53889\">\u003cimg class=\"size-full wp-image-53889\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Clostridium_difficile_01.png\" alt='C. difficile can cause some nasty problems if left unchecked by \"good\" bacteria. (Photo: Centers for Disease Control)' width=\"320\" height=\"auto\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/05/Clostridium_difficile_01.png 447w, https://ww2.kqed.org/app/uploads/sites/39/2013/05/Clostridium_difficile_01-400x268.png 400w\" sizes=\"(max-width: 447px) 100vw, 447px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">C. difficile can cause some nasty problems if left unchecked by \"good\" bacteria. (Photo: Centers for Disease Control)\u003c/figcaption>\u003c/figure>\n\u003cdiv>\u003cstrong>\u003cem>Clostridium difficile\u003c/em>\u003c/strong>\u003c/div>\n\u003cp>The “good” bacteria in your gut often keep bad stuff at bay. When the good guys are destroyed (possibly with antibiotics), \u003cem>C. difficile\u003c/em> takes over, which can cause severe diarrhea or deadly inflammation of the colon. The condition most commonly affects hospitalized older adults or those in long-term care. The cure: more antibiotics — or a fecal transplant.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.mayoclinic.com/health/c-difficile/DS00736\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003cstrong>Bifidobacterium\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_53888\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/bifidobacterium/\" rel=\"attachment wp-att-53888\">\u003cimg class=\"size-full wp-image-53888\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/Bifidobacterium.jpg\" alt=\"Bifidobacterium lives throughout the body and can be damaged by antibiotic treatments. (Photo: Wikimedia Commons)\" width=\"320\" height=\"auto\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Bifidobacterium lives throughout the body and can be damaged by antibiotic treatments. (Photo: Wikimedia Commons)\u003c/figcaption>\u003c/figure>\n\u003cp dir=\"ltr\">The gut biota ecosystem is a dramatically changing environment in the first two years of life. Bifidobacterium include a range of bacteria species that exist symbiotically throughout our bodies. But the evolution of Bifidobacterium in infant bodies can be stunted by early antibiotic treatment. The bacteria are linked with many probiotic benefits, and scientists do not yet understand the long-term health consequences of reducing their numbers.\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/22948872\">Source\u003c/a>\u003c/em>\u003c/p>\n\u003cfigure id=\"attachment_53891\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/03/the-human-microbiome-a-rogues-gallery/p-ging/\" rel=\"attachment wp-att-53891\">\u003cimg class=\"size-full wp-image-53891\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/05/p-ging.jpg\" alt=\"P. gingivalis can make your teeth fall out. (Photo: Flickr user AJC1)\" width=\"320\" height=\"auto\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">P. gingivalis can make your teeth fall out. (Photo: Flickr user AJC1)\u003c/figcaption>\u003c/figure>\n\u003cp> \u003c/p>\n\u003cp>\u003cstrong>\u003cem>Porphyromonas gingivalis\u003c/em>\u003c/strong>\u003c/p>\n\u003cp>Did you brush your teeth this morning? The microflora in our mouths can cause some real problems. Take \u003cem>P. gingivalis\u003c/em> (pictured). The bacteria places a role in the onset of periodontitis, an inflammation of the gums that causes teeth to fall out. \u003cem>P. gingivalis\u003c/em> is also associated with rheumatoid arthritis and heart disease. It’s less abundant in the mouth than, say, \u003cem>Streptococcus parasanguinis\u003c/em>. Those bacteria colonize the surface of your teeth, forming plaque.\u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp> \u003c/p>\n\u003cp>\u003c/p>\n\u003cp> \u003c/p>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Top Cats: How Pumas and Other Apex Predators' Populations Affect The Big Biodiversity Picture",
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"content": "\u003cfigure id=\"attachment_53676\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/01/top-cats-how-pumas-and-other-apex-predators-populations-affect-the-big-biodiversity-picture/kumalion/\" rel=\"attachment wp-att-53676\">\u003cimg class=\"size-large wp-image-53676\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/kumalion-640x360.jpg\" alt=\"The cat of many names--mountain lion, puma, cougar, catamount, panther, to name a few--speaks to the once widespread distribution of Puma concolor across the continent. The wide-ranging carnivore can adapt to nearly any landscape. It remains to be seen whether it can adapt to the expansive activities of the human being.\" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The cat of many names--mountain lion, puma, cougar, catamount, panther, to name a few--speaks to the once widespread distribution of Puma concolor across the continent. The wide-ranging carnivore can adapt to nearly any landscape. It remains to be seen whether it can adapt to the expansive activities of the human being. Photo: Liza Gross\u003c/figcaption>\u003c/figure>\n\u003cp>Two years ago, a stellar cast of ecologists changed the way conservation scientists think about biodiversity. As we tumble headlong into the sixth great extinction, biologists have focused largely on protecting regions with the highest number of species. By saving the most species, the thinking goes, you’ll conserve the greatest number of ecological interactions and so the greatest biodiversity. But in \u003ca href=\"http://media.longnow.org/files/2/REVIVE/Estes%20et%20al%20(w%20Berger)%20Trophic%20Downgrading%20%20-%20Science%202011.pdf\">a study that drew on ecological theory\u003c/a> and contemporary studies of apex predators like wolves and pumas, the all-star team of ecologists found that some species matter more than others. Losing top predators, they argued, can have far-reaching, irreversible effects on the structure, function and biodiversity of ecosystems.\u003c/p>\n\u003cp>Ecological theory predicts that changes in the abundance and distribution of top predators can cause substantial shifts in ecosystems. And recent studies—many published in the new millennium—have shown how theoretical predictions play out on the landscape. The collapse of \u003ca href=\"http://www.sefs.washington.edu/classes.esrm.450/Anthony.pdf\">sea otter populations\u003c/a> on Amchitka Island in the Aleutian Islands decimated kelp forests by allowing unfettered expansion of sea urchins, the otters’ main food. The loss of wolves in Yellowstone’s Lamar River Valley famously allowed elk to forage with abandon, arresting the development of streamside willows and other riparian vegetation. In Venezuela, forests without jaguars, pumas and eagles had almost no vegetative underbrush compared to the lush understory in forests where predators kept ungulate herbivores in check.\u003c/p>\n\u003cp>But, according to the study, the loss of large top predators can also lead to soaring rates of wildfires, infectious disease and carbon emissions, and degrade water quality and nutrient cycles.\u003c/p>\n\u003cp>These “top down” trophic cascades, which the ecologists dubbed “trophic downgrading,” have been documented from the poles to the equators and every major biome in between, making the loss of top predators, they wrote, “arguably humankind’s most pervasive influence on the natural world.\" Earth has weathered five mass extinctions but never before at the hands of one species—human beings. And we humans seem hell bent on clearing the Earth of larger bodied apex predators.\u003c/p>\n\u003cp>I considered all this as I read a new paper from \u003ca href=\"http://wildlife.ucsc.edu/\">wildlife ecologist Chris Wilmer’s lab\u003c/a> (\u003ca href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060590\">published last week in PLOS ONE\u003c/a>) that looks at how human development affects pumas. Like most large carnivores, pumas need vast territories to hunt, find mates and raise young. Pumas living in the San Francisco Bay Area have no such luck. Wilmers, an associate professor of environmental studies at the University of California-Santa Cruz, has been studying the effects of habitat fragmentation on the behavior, ecology and even the physiology of \u003ca href=\"http://santacruzpumas.org/\">pumas around the Santa Cruz Mountains.\u003c/a> He develops cutting-edge GPS collars to track both the location and behavior of his animals.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Fragmented landscapes often pave the way to extinction for wide-ranging large carnivores like pumas, with cascading effects. Freed from the threat of top predators, smaller carnivores like foxes increase in number, driving declines in birds and small mammals. But habitat fragmentation can produce effects similar to extinction because large predators tend to avoid small fragmented parcels. Given the heterogeneous patterns of human developments—with houses and other structures interspersed among natural areas—predicting how animals might respond, and with what consequences, presents a serious challenge.\u003c/p>\n\u003cp>Since pumas make risk-benefit calculations just like the rest of us and typically avoid humans—\u003ca href=\"http://www.vetmed.ucdavis.edu/whc/programs/mountain_lions/humans.cfm\">their biggest cause of death, aside from roads\u003c/a>—Wilmers wanted to know what factors govern their decisions. He and his team figured the cats would steer clear of neighborhoods, where they’d risk seeing their nemesis in various activities, more than roads, where traffic can be sporadic. And they predicted the cats would respond differently depending on their reproductive status. If running into humans meant losing a meal, that would prove less costly from an evolutionary perspective, than if it meant losing a chance to mate or raise young—since, as any evolutionary biologist will tell you, we exist primarily to reproduce.\u003c/p>\n\u003cp>The team combined their GPS data with field visits to determine whether cats were simply going about their business—that is, feeding (based on the analysis of GPS data and confirmed by finding prey remains) or moving about the landscape (GPS readings not linked to kill or den sites)—or engaged in reproductive behavior—denning (indicated by a female staying within a spot and making repeated return visits) or communicating (indicated by \u003ca href=\"http://www.youtube.com/watch?feature=player_embedded&v=A348t8_I8d4\">“scrapes,”\u003c/a> urine-soaked leaves and debris mounded with the hind feet, the puma version of “here’s my number”).\u003c/p>\n\u003cp>As predicted, the cats’ response to developments varied with their reproductive status. The data collected on their 20 collared pumas (12 females and 8 males) showed that the animals give human developments a wider berth when engaged in reproductive behaviors. Given how frequently human run-ins result in death for pumas around the Bay Area, it’s not surprising that evolutionary pressures selected against placing the next generation at risk. Similarly, the cats seem to have learned that placing their calling card near trails leaves them vulnerable to destruction by hikers and bikers.\u003c/p>\n\u003cp>Still, it appears that taking care of large cubs makes mom willing to take more risks. The team found that females with dependent young showed higher tolerance for residential developments than males, possibly because they can’t afford to be choosy about where they find prey. Still, one male in the study did go near developments—a young male seeking new territory—an extremely risky behavior that the sexually \u003ca href=\"http://www.sfgate.com/green/article/Mountain-lions-straying-into-more-urban-areas-3164598.php\">immature male shot in Berkeley’s Gourmet Ghetto\u003c/a> learned too late.\u003c/p>\n\u003cp>There’s no doubt that our behavior influences the big cats’ behavior. If you live on the edge of puma habitat and plant lush gardens, you’ll attract deer—and likely their ancient predator. If you don’t safeguard your goats and sheep in enclosed pens at night, you’re just asking for trouble. An astonishing \u003ca href=\"http://santacruzpumas.org/blog/\">eight of the 11 adult pumas\u003c/a> the team studied were shot for attacking livestock.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>By understanding where, when and how pumas use their increasingly fragmented habitat, Wilmers and his team can predict how they might respond as development continues. They can also predict, and hopefully mitigate, likely conflicts between humans and the increasingly boxed-in carnivores. But ecologists, even the best ecologists, can do only so much. They need the rest of us to decide whether we’re ready to reverse the trophic downgrading of the planet before it’s too late.\u003c/p>\n\n",
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"excerpt": "Apex predators exert far-reaching effects on ecosystems that surface just decades after their disappearance. Santa Cruz researchers hope to understand how human activities and development affect how pumas use the landscape to help mitigate conflicts and plan for the species' long-term survival.",
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"description": "Apex predators exert far-reaching effects on ecosystems that surface just decades after their disappearance. Santa Cruz researchers hope to understand how human activities and development affect how pumas use the landscape to help mitigate conflicts and plan for the species' long-term survival.",
"title": "Top Cats: How Pumas and Other Apex Predators' Populations Affect The Big Biodiversity Picture | KQED",
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"headline": "Top Cats: How Pumas and Other Apex Predators' Populations Affect The Big Biodiversity Picture",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_53676\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/05/01/top-cats-how-pumas-and-other-apex-predators-populations-affect-the-big-biodiversity-picture/kumalion/\" rel=\"attachment wp-att-53676\">\u003cimg class=\"size-large wp-image-53676\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/kumalion-640x360.jpg\" alt=\"The cat of many names--mountain lion, puma, cougar, catamount, panther, to name a few--speaks to the once widespread distribution of Puma concolor across the continent. The wide-ranging carnivore can adapt to nearly any landscape. It remains to be seen whether it can adapt to the expansive activities of the human being.\" width=\"640\" height=\"360\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The cat of many names--mountain lion, puma, cougar, catamount, panther, to name a few--speaks to the once widespread distribution of Puma concolor across the continent. The wide-ranging carnivore can adapt to nearly any landscape. It remains to be seen whether it can adapt to the expansive activities of the human being. Photo: Liza Gross\u003c/figcaption>\u003c/figure>\n\u003cp>Two years ago, a stellar cast of ecologists changed the way conservation scientists think about biodiversity. As we tumble headlong into the sixth great extinction, biologists have focused largely on protecting regions with the highest number of species. By saving the most species, the thinking goes, you’ll conserve the greatest number of ecological interactions and so the greatest biodiversity. But in \u003ca href=\"http://media.longnow.org/files/2/REVIVE/Estes%20et%20al%20(w%20Berger)%20Trophic%20Downgrading%20%20-%20Science%202011.pdf\">a study that drew on ecological theory\u003c/a> and contemporary studies of apex predators like wolves and pumas, the all-star team of ecologists found that some species matter more than others. Losing top predators, they argued, can have far-reaching, irreversible effects on the structure, function and biodiversity of ecosystems.\u003c/p>\n\u003cp>Ecological theory predicts that changes in the abundance and distribution of top predators can cause substantial shifts in ecosystems. And recent studies—many published in the new millennium—have shown how theoretical predictions play out on the landscape. The collapse of \u003ca href=\"http://www.sefs.washington.edu/classes.esrm.450/Anthony.pdf\">sea otter populations\u003c/a> on Amchitka Island in the Aleutian Islands decimated kelp forests by allowing unfettered expansion of sea urchins, the otters’ main food. The loss of wolves in Yellowstone’s Lamar River Valley famously allowed elk to forage with abandon, arresting the development of streamside willows and other riparian vegetation. In Venezuela, forests without jaguars, pumas and eagles had almost no vegetative underbrush compared to the lush understory in forests where predators kept ungulate herbivores in check.\u003c/p>\n\u003cp>But, according to the study, the loss of large top predators can also lead to soaring rates of wildfires, infectious disease and carbon emissions, and degrade water quality and nutrient cycles.\u003c/p>\n\u003cp>These “top down” trophic cascades, which the ecologists dubbed “trophic downgrading,” have been documented from the poles to the equators and every major biome in between, making the loss of top predators, they wrote, “arguably humankind’s most pervasive influence on the natural world.\" Earth has weathered five mass extinctions but never before at the hands of one species—human beings. And we humans seem hell bent on clearing the Earth of larger bodied apex predators.\u003c/p>\n\u003cp>I considered all this as I read a new paper from \u003ca href=\"http://wildlife.ucsc.edu/\">wildlife ecologist Chris Wilmer’s lab\u003c/a> (\u003ca href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060590\">published last week in PLOS ONE\u003c/a>) that looks at how human development affects pumas. Like most large carnivores, pumas need vast territories to hunt, find mates and raise young. Pumas living in the San Francisco Bay Area have no such luck. Wilmers, an associate professor of environmental studies at the University of California-Santa Cruz, has been studying the effects of habitat fragmentation on the behavior, ecology and even the physiology of \u003ca href=\"http://santacruzpumas.org/\">pumas around the Santa Cruz Mountains.\u003c/a> He develops cutting-edge GPS collars to track both the location and behavior of his animals.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Fragmented landscapes often pave the way to extinction for wide-ranging large carnivores like pumas, with cascading effects. Freed from the threat of top predators, smaller carnivores like foxes increase in number, driving declines in birds and small mammals. But habitat fragmentation can produce effects similar to extinction because large predators tend to avoid small fragmented parcels. Given the heterogeneous patterns of human developments—with houses and other structures interspersed among natural areas—predicting how animals might respond, and with what consequences, presents a serious challenge.\u003c/p>\n\u003cp>Since pumas make risk-benefit calculations just like the rest of us and typically avoid humans—\u003ca href=\"http://www.vetmed.ucdavis.edu/whc/programs/mountain_lions/humans.cfm\">their biggest cause of death, aside from roads\u003c/a>—Wilmers wanted to know what factors govern their decisions. He and his team figured the cats would steer clear of neighborhoods, where they’d risk seeing their nemesis in various activities, more than roads, where traffic can be sporadic. And they predicted the cats would respond differently depending on their reproductive status. If running into humans meant losing a meal, that would prove less costly from an evolutionary perspective, than if it meant losing a chance to mate or raise young—since, as any evolutionary biologist will tell you, we exist primarily to reproduce.\u003c/p>\n\u003cp>The team combined their GPS data with field visits to determine whether cats were simply going about their business—that is, feeding (based on the analysis of GPS data and confirmed by finding prey remains) or moving about the landscape (GPS readings not linked to kill or den sites)—or engaged in reproductive behavior—denning (indicated by a female staying within a spot and making repeated return visits) or communicating (indicated by \u003ca href=\"http://www.youtube.com/watch?feature=player_embedded&v=A348t8_I8d4\">“scrapes,”\u003c/a> urine-soaked leaves and debris mounded with the hind feet, the puma version of “here’s my number”).\u003c/p>\n\u003cp>As predicted, the cats’ response to developments varied with their reproductive status. The data collected on their 20 collared pumas (12 females and 8 males) showed that the animals give human developments a wider berth when engaged in reproductive behaviors. Given how frequently human run-ins result in death for pumas around the Bay Area, it’s not surprising that evolutionary pressures selected against placing the next generation at risk. Similarly, the cats seem to have learned that placing their calling card near trails leaves them vulnerable to destruction by hikers and bikers.\u003c/p>\n\u003cp>Still, it appears that taking care of large cubs makes mom willing to take more risks. The team found that females with dependent young showed higher tolerance for residential developments than males, possibly because they can’t afford to be choosy about where they find prey. Still, one male in the study did go near developments—a young male seeking new territory—an extremely risky behavior that the sexually \u003ca href=\"http://www.sfgate.com/green/article/Mountain-lions-straying-into-more-urban-areas-3164598.php\">immature male shot in Berkeley’s Gourmet Ghetto\u003c/a> learned too late.\u003c/p>\n\u003cp>There’s no doubt that our behavior influences the big cats’ behavior. If you live on the edge of puma habitat and plant lush gardens, you’ll attract deer—and likely their ancient predator. If you don’t safeguard your goats and sheep in enclosed pens at night, you’re just asking for trouble. An astonishing \u003ca href=\"http://santacruzpumas.org/blog/\">eight of the 11 adult pumas\u003c/a> the team studied were shot for attacking livestock.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>By understanding where, when and how pumas use their increasingly fragmented habitat, Wilmers and his team can predict how they might respond as development continues. They can also predict, and hopefully mitigate, likely conflicts between humans and the increasingly boxed-in carnivores. But ecologists, even the best ecologists, can do only so much. They need the rest of us to decide whether we’re ready to reverse the trophic downgrading of the planet before it’s too late.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"disqusTitle": "Fund Basic Research, It’s For Your Own Good",
"title": "Fund Basic Research, It’s For Your Own Good",
"headTitle": "QUEST | KQED Science",
"content": "\u003cfigure id=\"attachment_52581\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/04/22/fund-basic-research-its-for-your-own-good/lamppost/\" rel=\"attachment wp-att-52581\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Lamppost.jpg\" alt=\"Basic research shines light on parts of science we didn't even know we should be looking at. Image courtesy of Wikimedia Commons.\" width=\"640\" height=\"362\" class=\"size-full wp-image-52581\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Lamppost.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Lamppost-400x226.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Basic research shines light on parts of science we didn't even know we should be looking at. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Lamp-post_silhouette_(3795639484).jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>The budget proposal by the Obama administration is a mixed bag in terms of \u003ca href=\"http://www.nature.com/news/a-back-seat-for-basic-science-1.12803\">funding for science\u003c/a>. Targeted research received some OK gains but basic research was left with the same or even less money than the previous year. If this trend continues, it won’t just be basic research that takes a hit. It’ll be your health and the U.S. economy too.\u003c/p>\n\u003cp>I know, I know, a scientist bemoaning a cut in funding -- talk about someone with a vested interest! But hear me out.\u003c/p>\n\u003cp>In some ways this funding proposal is understandable. We have a dwindling pot of money and we want to fund what will be most likely to pay off. The problem is that this approach keeps science from finding completely new things that will lead to new approaches to treating diseases, identifying new energy sources and so on. We won't make any dramatic leaps in knowledge that fundamentally change how we address our problems.\u003c/p>\n\u003cp>Funding predominantly targeted research is like looking for your car keys only in lighted areas of the street. You are missing a whole lot places where the keys could be. Science is similar. Basic research is like adding new light posts—it opens up areas of research we didn’t even know we could explore.\u003c/p>\n\u003cp>I have a listed a few such findings off the top of my head. Because I’m more of a molecular biologist/geneticist, I’ve focused on these topics. There are undoubtedly lots of other examples from this and other areas that I haven’t included. Please feel free to add more to the comments section if you’d like.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>Cell cycle regulators\u003c/strong>. Cancer happens when a cell grows out of control and/or refuses to die. Our cells have all sorts of controls in place to keep cells growing and dividing when they should and to also stop growing and even to die when they should too. The key regulators in this process were originally found in the humble baker’s yeast, Saccharomyces cerevisiae. We found them more easily in yeast because of the unique properties of this model system (easily manipulated genetics, fast growing, etc.). Because of that initial basic research, we were able to study this aspect of cancer and begin to identify treatments based on these regulators much sooner than we otherwise would have.\u003c/p>\n\u003cp>\u003cstrong>Micro RNAs\u003c/strong>. Until the early 1990’s, RNA was mostly thought of as a passive molecule. Basically the instructions found in genes in DNA were copied into RNA. This mRNA was then translated into proteins using two other RNAs, tRNA and rRNA, and it was proteins that did all the heavy lifting in the cell.\u003c/p>\n\u003cp>Through the work done in a small, see-through worm called C. elegans, we discovered that tiny RNAs are actually important in controlling how much protein gets made from a gene. These microRNAs are used in people too and have been shown to be involved in a number of cancers. Not only that, but they are incredibly useful tools for exploring how genes work so we can find new targets to go after for cancer research. It would have taken a very long time to find them with targeted research and even longer to figure out they were significant and how they work without basic research. I am not sure we would have found out what they are and/or do for decades if we had just focused on people.\u003c/p>\n\u003cfigure id=\"attachment_52597\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/04/22/fund-basic-research-its-for-your-own-good/insulin-bottle/\" rel=\"attachment wp-att-52597\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/insulin-bottle.gif\" alt=\"Without the basic research on enzymes that cut bacterial DNA at certain places and the research on little bits of self-replicating DNA called plasmids, we’d still be getting our insulin from pigs and cadavers.\" width=\"200\" height=\"208\" class=\"size-full wp-image-52597\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/insulin-bottle.gif 200w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/insulin-bottle-32x32.gif 32w\" sizes=\"(max-width: 200px) 100vw, 200px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Without the basic research on enzymes that cut bacterial DNA at certain places and the research on little bits of self-replicating DNA called plasmids, we’d still be getting our insulin from pigs and cadavers.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Genetic Engineering\u003c/strong>: What started out as some basic research on bacteria in the 1960’s and early 1970’s, turned into today’s genetic engineering. People who become anemic from cancer treatments can thank basic science for their EPO and people with diabetes can do the same for their insulin. Both are now grown in bacteria using the genetic engineering tools created from basic research. \u003c/p>\n\u003cp>And the list can go on and on. The human genome project has opened up so many avenues of research that we are still figuring out where to go with it all. The same is true for the basic research that identified stem cells, the structure of DNA, recombination and on and on.\u003c/p>\n\u003cp>If we had just focused on targeted research, we would have missed most of this or at least research would have been delayed by years or even decades. Sick people would have suffered longer because we didn’t fund basic research.\u003c/p>\n\u003cp>Of course I understand the quandary we are in here. If we have to choose between research on \u003ca href=\"http://phenomena.nationalgeographic.com/2013/03/25/ducks-meet-the-culture-wars/\">duck penises\u003c/a> and food stamps for poor families, food stamps would undoubtedly win. This is even if the duck research might help us understand and possible even better treat conditions like preeclampsia, a problem with high blood pressure that can happen with pregnancy.\u003c/p>\n\u003cp>But we do need to think about how we can get the most bang for our limited science research dollars. Can we free up some money by streamlining how scientists are funded? Should we change how we assess whether scientific research has been successful or not? Should we divvy up the money in different ways with an increased percentage going to basic research?\u003c/p>\n\u003cp>I don’t have the answers to these questions but the folks in Washington need to start thinking about this. I don’t think we want to give up our strong science position in the world just yet.\u003c/p>\n\u003cp>\u003ca href=\"http://www.lbl.gov/Education/ELSI/research-main.html\">More on applied vs. basic research\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://www.genomicron.evolverzone.com/2008/02/basic-research-is-lifeline-of-practical/\">Importance of basic research\u003c/a>\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_52581\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/04/22/fund-basic-research-its-for-your-own-good/lamppost/\" rel=\"attachment wp-att-52581\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/Lamppost.jpg\" alt=\"Basic research shines light on parts of science we didn't even know we should be looking at. Image courtesy of Wikimedia Commons.\" width=\"640\" height=\"362\" class=\"size-full wp-image-52581\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/Lamppost.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/Lamppost-400x226.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Basic research shines light on parts of science we didn't even know we should be looking at. Image courtesy of \u003ca href=\"http://commons.wikimedia.org/wiki/File:Lamp-post_silhouette_(3795639484).jpg\">Wikimedia Commons\u003c/a>.\u003c/figcaption>\u003c/figure>\n\u003cp>The budget proposal by the Obama administration is a mixed bag in terms of \u003ca href=\"http://www.nature.com/news/a-back-seat-for-basic-science-1.12803\">funding for science\u003c/a>. Targeted research received some OK gains but basic research was left with the same or even less money than the previous year. If this trend continues, it won’t just be basic research that takes a hit. It’ll be your health and the U.S. economy too.\u003c/p>\n\u003cp>I know, I know, a scientist bemoaning a cut in funding -- talk about someone with a vested interest! But hear me out.\u003c/p>\n\u003cp>In some ways this funding proposal is understandable. We have a dwindling pot of money and we want to fund what will be most likely to pay off. The problem is that this approach keeps science from finding completely new things that will lead to new approaches to treating diseases, identifying new energy sources and so on. We won't make any dramatic leaps in knowledge that fundamentally change how we address our problems.\u003c/p>\n\u003cp>Funding predominantly targeted research is like looking for your car keys only in lighted areas of the street. You are missing a whole lot places where the keys could be. Science is similar. Basic research is like adding new light posts—it opens up areas of research we didn’t even know we could explore.\u003c/p>\n\u003cp>I have a listed a few such findings off the top of my head. Because I’m more of a molecular biologist/geneticist, I’ve focused on these topics. There are undoubtedly lots of other examples from this and other areas that I haven’t included. Please feel free to add more to the comments section if you’d like.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>Cell cycle regulators\u003c/strong>. Cancer happens when a cell grows out of control and/or refuses to die. Our cells have all sorts of controls in place to keep cells growing and dividing when they should and to also stop growing and even to die when they should too. The key regulators in this process were originally found in the humble baker’s yeast, Saccharomyces cerevisiae. We found them more easily in yeast because of the unique properties of this model system (easily manipulated genetics, fast growing, etc.). Because of that initial basic research, we were able to study this aspect of cancer and begin to identify treatments based on these regulators much sooner than we otherwise would have.\u003c/p>\n\u003cp>\u003cstrong>Micro RNAs\u003c/strong>. Until the early 1990’s, RNA was mostly thought of as a passive molecule. Basically the instructions found in genes in DNA were copied into RNA. This mRNA was then translated into proteins using two other RNAs, tRNA and rRNA, and it was proteins that did all the heavy lifting in the cell.\u003c/p>\n\u003cp>Through the work done in a small, see-through worm called C. elegans, we discovered that tiny RNAs are actually important in controlling how much protein gets made from a gene. These microRNAs are used in people too and have been shown to be involved in a number of cancers. Not only that, but they are incredibly useful tools for exploring how genes work so we can find new targets to go after for cancer research. It would have taken a very long time to find them with targeted research and even longer to figure out they were significant and how they work without basic research. I am not sure we would have found out what they are and/or do for decades if we had just focused on people.\u003c/p>\n\u003cfigure id=\"attachment_52597\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/quest/2013/04/22/fund-basic-research-its-for-your-own-good/insulin-bottle/\" rel=\"attachment wp-att-52597\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/insulin-bottle.gif\" alt=\"Without the basic research on enzymes that cut bacterial DNA at certain places and the research on little bits of self-replicating DNA called plasmids, we’d still be getting our insulin from pigs and cadavers.\" width=\"200\" height=\"208\" class=\"size-full wp-image-52597\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/insulin-bottle.gif 200w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/insulin-bottle-32x32.gif 32w\" sizes=\"(max-width: 200px) 100vw, 200px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Without the basic research on enzymes that cut bacterial DNA at certain places and the research on little bits of self-replicating DNA called plasmids, we’d still be getting our insulin from pigs and cadavers.\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Genetic Engineering\u003c/strong>: What started out as some basic research on bacteria in the 1960’s and early 1970’s, turned into today’s genetic engineering. People who become anemic from cancer treatments can thank basic science for their EPO and people with diabetes can do the same for their insulin. Both are now grown in bacteria using the genetic engineering tools created from basic research. \u003c/p>\n\u003cp>And the list can go on and on. The human genome project has opened up so many avenues of research that we are still figuring out where to go with it all. The same is true for the basic research that identified stem cells, the structure of DNA, recombination and on and on.\u003c/p>\n\u003cp>If we had just focused on targeted research, we would have missed most of this or at least research would have been delayed by years or even decades. Sick people would have suffered longer because we didn’t fund basic research.\u003c/p>\n\u003cp>Of course I understand the quandary we are in here. If we have to choose between research on \u003ca href=\"http://phenomena.nationalgeographic.com/2013/03/25/ducks-meet-the-culture-wars/\">duck penises\u003c/a> and food stamps for poor families, food stamps would undoubtedly win. This is even if the duck research might help us understand and possible even better treat conditions like preeclampsia, a problem with high blood pressure that can happen with pregnancy.\u003c/p>\n\u003cp>But we do need to think about how we can get the most bang for our limited science research dollars. Can we free up some money by streamlining how scientists are funded? Should we change how we assess whether scientific research has been successful or not? Should we divvy up the money in different ways with an increased percentage going to basic research?\u003c/p>\n\u003cp>I don’t have the answers to these questions but the folks in Washington need to start thinking about this. I don’t think we want to give up our strong science position in the world just yet.\u003c/p>\n\u003cp>\u003ca href=\"http://www.lbl.gov/Education/ELSI/research-main.html\">More on applied vs. basic research\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://www.genomicron.evolverzone.com/2008/02/basic-research-is-lifeline-of-practical/\">Importance of basic research\u003c/a>\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>Two Bay Area kids are \u003ca href=\"http://www.stopextinction.org/esd/434-2013-art.html\">semi-finalists\u003c/a> in a national art contest celebrating endangered species.\u003c/p>\n\u003cp>First-grader Hannah Chacko, of San Francisco, turned in this colorful drawing of the endangered San Francisco garter snake. (Perhaps a new t-shirt design for the city’s \u003ca href=\"http://www.sfgate.com/bayarea/article/Judge-says-golf-can-stay-at-Sharp-Park-4101144.php\">Sharp Park Golf Course\u003c/a>?) \u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/K-2HannahChacko.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/K-2HannahChacko-224x169.jpg\" alt=\"H\" width=\"224\" height=\"169\" class=\"alignleft size-thumbnail wp-image-52787\">\u003c/a>\u003c/p>\n\u003cp>Foster City’s Kevin Huo, an eighth grader, submitted one of the most impressionistic entries in the bunch: this vivid depiction of an albatross – legendary protector of sailors -- soaring above a boat. \u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/6-8-Kevin-Huo.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/6-8-Kevin-Huo-130x169.jpg\" alt=\"Albatross, Kevin Huo\" width=\"130\" height=\"169\" class=\"alignright size-thumbnail wp-image-52785\">\u003c/a>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>The contest is sponsored by the U.S. Fish and Wildlife Service, the Endangered Species Coalition, the Association of Zoos and Aquariums and the International Child Art Foundation. \u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/K-2-Ava-Bribiesco.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/K-2-Ava-Bribiesco-221x169.jpg\" alt=\"T\" width=\"221\" height=\"169\" class=\"alignleft size-thumbnail wp-image-52786\">\u003c/a>\u003c/p>\n\u003cp>Top honors went to kindergartener Ava Bribiesco of St. Louis, Missouri, for her collage of the American Burying Beetle. \u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003c/p>\n\n",
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"disqusTitle": "Brain Mapping: From the Basics to Science Fiction",
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"content": "\u003cp>http://www.kqed.org/.stream/anon/radio/quest/2013/04/20130422science.mp3\u003c/p>\n\u003cfigure id=\"attachment_52713\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003cimg class=\"size-full wp-image-52713\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/brains.jpg\" alt=\"fMRI brain scans. (David Feinberg/UC Berkeley)\" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/brains.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/brains-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">fMRI brain scans. (David Feinberg/UC Berkeley)\u003c/figcaption>\u003c/figure>\n\u003cp>Get ready for the year – or the decade – of the brain.\u003c/p>\n\u003cp>President Obama recently announced what he called the next “Great American Project”: $100 million, plus private investment, to study what he called “that matter between our ears.”\u003c/p>\n\u003cp>Much of this work is already happening here in the Bay Area, where neuroscientists are starting small and dreaming big.\u003cbr>\n\u003cstrong>\u003cbr>\nCracking the Code\u003c/strong>\u003c/p>\n\u003cp>There's an idea about the brain that you hear a lot: That it’s akin to a language. If you could just figure out the meaning of every letter, you could read it and say – or do – anything.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>“Think about what we could do once we do crack this code,” said President Obama in announcing his BRAIN initiative, which he’ll also have to sell to Congress.\u003c/p>\n\u003cp>“Imagine if no family had to feel helpless watching a loved one disappear behind the mask of Parkinson’s or struggle in the grip of epilepsy. Imagine if we could reverse traumatic brain injury or PTSD for our veterans who are coming home.”\u003c/p>\n\u003cp>But before any of that can be achieved – even if it can be achieved – we have to understand the brain first.\u003c/p>\n\u003cp>“The human brain is the most complicated known entity in the universe,” says William Newsome, a Stanford University professor of neurobiology and co-chair of the president’s BRAIN Initiative.\u003c/p>\n\u003cp>It's Newsome’s job to figure out what this mapping plan is all about.\u003cstrong>\u003cem> \u003c/em>\u003c/strong>\u003cbr>\n\u003cstrong>\u003cbr>\n\"The most complex entity in the universe\"\u003c/strong>\u003c/p>\n\u003cp>He says consider the numbers. There could be close to a hundred billion\u003cem> \u003c/em>neurons, or nerve cells, in the human brain. And somewhere in the neighborhood of a thousand trillion connections, zapping little jolts of information back and forth from cell to cell.\u003c/p>\n\u003cp>Mapping at that level is not going to happen anytime soon, Newsome says.\u003c/p>\n\u003cp>“We are not going to solve and completely understand the human brain in ten years, or probably not even in 100 years,\" says Newsome. “It may take us a couple hundred years.\"\u003c/p>\n\u003cp>That’s a long time, which is one reason the project has been criticized as too vague.\u003c/p>\n\u003cp>If the goal of the BRAIN initiative isn't to fully map the brain or to cure a specific disease, what is it? And without a specific goal, how do you decide what kind of research to focus on?\u003c/p>\n\u003cp>It’s like trying to understand a beach. Do you count the grains of sand? Or study satellite photos of the entire coastline?\u003c/p>\n\u003cp>Somewhere near the satellite level is the work happening in UC Berkeley psychology professor Jack Gallant’s lab.\u003c/p>\n\u003cp>A graduate student named James is trying to stay as still as possible inside a functional MRI machine. When James squeezes a ball, the machine beeps steadily.\u003c/p>\n\u003cp>“It’s the sound of data,” Gallant says.\u003cbr>\n\u003cstrong>\u003cbr>\nMind Reading, Circa 2013\u003c/strong>\u003c/p>\n\u003cp>Gallant points to a computer monitor where, every two seconds, another crisp, black and white image of James’ brain refreshes itself.\u003c/p>\n\u003cp>“Here’s the cortex, the cerebellum back here. This is the brain stem, the thalamus,” Gallant says.\u003c/p>\n\u003cp>Using the fMRI, Gallant’s lab has been able to record what happens inside subjects’ brains while they watch movies, and then translate those responses into images.\u003c/p>\n\u003cp>These reconstructed videos are blurry but remarkable, about as close to mind-reading as we get in 2013. Gallant says in theory, this is just the beginning.\u003c/p>\n\u003cp>“In principle, it’s probably possible to reconstruct any activity in your brain that reflects ongoing conscious brain processes,” he said.\u003c/p>\n\u003cp>[youtube=http://www.youtube.com/watch?v=nsjDnYxJ0bo]\u003c/p>\n\u003cp>Any conscious thought could, one day, be visible to the outside world: a memory, a dream or your private, internal dialogues.\u003c/p>\n\u003cp>“We have this little person in our head that talks to us all the time,” says Gallant. “There’s no reason we shouldn’t be able to reconstruct that.”\u003c/p>\n\u003cp>As amazing – and scary – as this is, Gallant and others are quick to point out that the fMRI is full of limitations. For example, it doesn’t actually show neurons, let alone the connections between them. To be able to easily watch human neurons in action would take a machine that hasn’t been invented yet.\u003c/p>\n\u003cp>“If we knew what that technology will be, we would invent it today,” Gallant said.\u003c/p>\n\u003cp>So the BRAIN Initiative is almost certainly going to involve engineers building better machines.\u003c/p>\n\u003cp>It’ll also involve work that has seemingly very little to do with humans at all. This work is a lot closer to the grain of sand level.\u003c/p>\n\u003cp>\u003cstrong>\u003cbr>\nStarting Small, Dreaming Big\u003c/strong>\u003c/p>\n\u003cp>John Ngai, director of UC Berkeley’s Helen Wills Neuroscience Institute, studies the olfactory system of – among other things – zebrafish.\u003c/p>\n\u003cp>Ngai wants to understand what happens in the brain of a zebrafish when it detects pheromones that signal danger. When the fish smell this pheromone, they dive to the bottom of the tank and hide.\u003c/p>\n\u003cp>Which of the zebra fish’s 100,000 or so neurons are driving this reaction and how?\u003c/p>\n\u003cp>If Ngai’s lab can figure this out, they’d have a working model for how information in a brain translates into behavior. And eventually not just for zebrafish.\u003c/p>\n\u003cp>Newsome, the head of the BRAIN Initiative, says\u003cstrong> \u003c/strong>fast-forward this line of work a generation or a few, and maybe you're closer to curing diseases like Alzheimer’s. Maybe you’ve even started to answer bigger questions.\u003c/p>\n\u003cp>Questions like, says Newsome, “why do I make so many mistakes that I know perfectly well are avoidable? Why do I hurt people that I love? Why do I turn left at some corner when I knew perfectly well that I should have turned right? What is it up there inside our head that produce emotions?”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Big questions that will have to start with very small answers.\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_52713\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003cimg class=\"size-full wp-image-52713\" src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/brains.jpg\" alt=\"fMRI brain scans. (David Feinberg/UC Berkeley)\" width=\"640\" height=\"360\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/brains.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/brains-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">fMRI brain scans. (David Feinberg/UC Berkeley)\u003c/figcaption>\u003c/figure>\n\u003cp>Get ready for the year – or the decade – of the brain.\u003c/p>\n\u003cp>President Obama recently announced what he called the next “Great American Project”: $100 million, plus private investment, to study what he called “that matter between our ears.”\u003c/p>\n\u003cp>Much of this work is already happening here in the Bay Area, where neuroscientists are starting small and dreaming big.\u003cbr>\n\u003cstrong>\u003cbr>\nCracking the Code\u003c/strong>\u003c/p>\n\u003cp>There's an idea about the brain that you hear a lot: That it’s akin to a language. If you could just figure out the meaning of every letter, you could read it and say – or do – anything.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“Think about what we could do once we do crack this code,” said President Obama in announcing his BRAIN initiative, which he’ll also have to sell to Congress.\u003c/p>\n\u003cp>“Imagine if no family had to feel helpless watching a loved one disappear behind the mask of Parkinson’s or struggle in the grip of epilepsy. Imagine if we could reverse traumatic brain injury or PTSD for our veterans who are coming home.”\u003c/p>\n\u003cp>But before any of that can be achieved – even if it can be achieved – we have to understand the brain first.\u003c/p>\n\u003cp>“The human brain is the most complicated known entity in the universe,” says William Newsome, a Stanford University professor of neurobiology and co-chair of the president’s BRAIN Initiative.\u003c/p>\n\u003cp>It's Newsome’s job to figure out what this mapping plan is all about.\u003cstrong>\u003cem> \u003c/em>\u003c/strong>\u003cbr>\n\u003cstrong>\u003cbr>\n\"The most complex entity in the universe\"\u003c/strong>\u003c/p>\n\u003cp>He says consider the numbers. There could be close to a hundred billion\u003cem> \u003c/em>neurons, or nerve cells, in the human brain. And somewhere in the neighborhood of a thousand trillion connections, zapping little jolts of information back and forth from cell to cell.\u003c/p>\n\u003cp>Mapping at that level is not going to happen anytime soon, Newsome says.\u003c/p>\n\u003cp>“We are not going to solve and completely understand the human brain in ten years, or probably not even in 100 years,\" says Newsome. “It may take us a couple hundred years.\"\u003c/p>\n\u003cp>That’s a long time, which is one reason the project has been criticized as too vague.\u003c/p>\n\u003cp>If the goal of the BRAIN initiative isn't to fully map the brain or to cure a specific disease, what is it? And without a specific goal, how do you decide what kind of research to focus on?\u003c/p>\n\u003cp>It’s like trying to understand a beach. Do you count the grains of sand? Or study satellite photos of the entire coastline?\u003c/p>\n\u003cp>Somewhere near the satellite level is the work happening in UC Berkeley psychology professor Jack Gallant’s lab.\u003c/p>\n\u003cp>A graduate student named James is trying to stay as still as possible inside a functional MRI machine. When James squeezes a ball, the machine beeps steadily.\u003c/p>\n\u003cp>“It’s the sound of data,” Gallant says.\u003cbr>\n\u003cstrong>\u003cbr>\nMind Reading, Circa 2013\u003c/strong>\u003c/p>\n\u003cp>Gallant points to a computer monitor where, every two seconds, another crisp, black and white image of James’ brain refreshes itself.\u003c/p>\n\u003cp>“Here’s the cortex, the cerebellum back here. This is the brain stem, the thalamus,” Gallant says.\u003c/p>\n\u003cp>Using the fMRI, Gallant’s lab has been able to record what happens inside subjects’ brains while they watch movies, and then translate those responses into images.\u003c/p>\n\u003cp>These reconstructed videos are blurry but remarkable, about as close to mind-reading as we get in 2013. Gallant says in theory, this is just the beginning.\u003c/p>\n\u003cp>“In principle, it’s probably possible to reconstruct any activity in your brain that reflects ongoing conscious brain processes,” he said.\u003c/p>\n\u003cp>\u003c/p>\u003cp>\u003cspan class='utils-parseShortcode-shortcodes-__youtubeShortcode__embedYoutube'>\n \u003cspan class='utils-parseShortcode-shortcodes-__youtubeShortcode__embedYoutubeInside'>\n \u003ciframe\n loading='lazy'\n class='utils-parseShortcode-shortcodes-__youtubeShortcode__youtubePlayer'\n type='text/html'\n src='//www.youtube.com/embed/nsjDnYxJ0bo'\n title='//www.youtube.com/embed/nsjDnYxJ0bo'\n allowfullscreen='true'\n style='border:0;'>\u003c/iframe>\n \u003c/span>\n \u003c/span>\u003c/p>\u003cp>\u003c/p>\n\u003cp>Any conscious thought could, one day, be visible to the outside world: a memory, a dream or your private, internal dialogues.\u003c/p>\n\u003cp>“We have this little person in our head that talks to us all the time,” says Gallant. “There’s no reason we shouldn’t be able to reconstruct that.”\u003c/p>\n\u003cp>As amazing – and scary – as this is, Gallant and others are quick to point out that the fMRI is full of limitations. For example, it doesn’t actually show neurons, let alone the connections between them. To be able to easily watch human neurons in action would take a machine that hasn’t been invented yet.\u003c/p>\n\u003cp>“If we knew what that technology will be, we would invent it today,” Gallant said.\u003c/p>\n\u003cp>So the BRAIN Initiative is almost certainly going to involve engineers building better machines.\u003c/p>\n\u003cp>It’ll also involve work that has seemingly very little to do with humans at all. This work is a lot closer to the grain of sand level.\u003c/p>\n\u003cp>\u003cstrong>\u003cbr>\nStarting Small, Dreaming Big\u003c/strong>\u003c/p>\n\u003cp>John Ngai, director of UC Berkeley’s Helen Wills Neuroscience Institute, studies the olfactory system of – among other things – zebrafish.\u003c/p>\n\u003cp>Ngai wants to understand what happens in the brain of a zebrafish when it detects pheromones that signal danger. When the fish smell this pheromone, they dive to the bottom of the tank and hide.\u003c/p>\n\u003cp>Which of the zebra fish’s 100,000 or so neurons are driving this reaction and how?\u003c/p>\n\u003cp>If Ngai’s lab can figure this out, they’d have a working model for how information in a brain translates into behavior. And eventually not just for zebrafish.\u003c/p>\n\u003cp>Newsome, the head of the BRAIN Initiative, says\u003cstrong> \u003c/strong>fast-forward this line of work a generation or a few, and maybe you're closer to curing diseases like Alzheimer’s. Maybe you’ve even started to answer bigger questions.\u003c/p>\n\u003cp>Questions like, says Newsome, “why do I make so many mistakes that I know perfectly well are avoidable? Why do I hurt people that I love? Why do I turn left at some corner when I knew perfectly well that I should have turned right? What is it up there inside our head that produce emotions?”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>Big questions that will have to start with very small answers.\u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/04/17/fire-safety-without-harm/fire/\" rel=\"attachment wp-att-52484\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/fire.jpg\" alt=\"fire\" width=\"640\" height=\"360\" class=\"alignleft size-full wp-image-52484\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/fire.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/fire-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003c/p>\n\u003cp>Last week, scientists and regulators from more than 20 countries gathered in San Francisco to discuss the latest research on flame retardants. \u003ca href=\"http://www.bfr2013.com/bfr2013_about.cfm\">The conference\u003c/a> lasted four days, but the theme of the meeting was clear from just a few talks: Do we need toxic chemicals to achieve fire safety?\u003c/p>\n\u003cp>For the past decade, scientists have voiced increasing concern about the potential health and environmental risks of these chemicals, which show up—and leach from—a growing number of consumer products. By now, most California consumers probably know that flame retardants permeate the foam in their couches and chairs, along with a surprising array of baby products. (On Monday, the \u003ca href=\"http://www.sfgate.com/health/article/Flame-retardants-to-be-removed-from-nap-mats-4436828.php\">San Francisco Chronicle noted\u003c/a> that at least some nap maps sold in the state will no longer contain flame retardants.)\u003c/p>\n\u003cp>As I reported yesterday in a \u003ca href=\"http://www.washingtonpost.com/national/health-science/flame-retardants-in-consumer-products-are-linked-to-health-and-cognitive-problems/2013/04/15/f5c7b2aa-8b34-11e2-9838-d62f083ba93f_story.html\">story for the Washington Post\u003c/a>, mounting evidence suggests that these brominated chemicals pose risks to human health. Californians carry among the highest levels of flame retardants in the world, which researchers attribute to a 70s-era flammability standard that requires foam products to resist an open flame for 12 seconds. Manufacturers typically used flame retardants to comply and many tailored their products to California’s standard—and considerable market share—to avoid double inventories. \u003c/p>\n\u003cp>Gov. Jerry Brown, concerned about the risks the chemicals pose to human health, \u003ca href=\"http://gov.ca.gov/news.php?id=17598\">called on the state agency\u003c/a> in charge of flammability standards to find a way to ensure fire safety without the need for toxic flame retardants. In March, the agency held \u003ca href=\"http://www.youtube.com/watch?v=_hOjKKdZR_s&feature=youtu.be\">a public hearing\u003c/a> on its new standard, revised to do just that. The new regulations go into effect July 2014.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Since 2011, when I started \u003ca href=\"http://www.environmentalhealthnews.org/ehs/news/2011/money-to-burn\">writing about flame retardants\u003c/a>, I’ve been struck by how the researchers studying these chemicals talk about their findings. Scientists tend to talk about their results in terms of what they don’t know and what new questions their studies raise. (All \u003ca href=\"http://www.scientificamerican.com/article.cfm?id=weak-link-fossil-darwinius\">exceptions duly noted\u003c/a>.) And those studying flame retardants do discuss their findings with all the usual caveats. But they also do something else. They tell me, \"We don’t like what we’re seeing.\" \u003c/p>\n\u003cp>A few weeks ago, I spoke with Heather Stapleton, a flame retardant expert at Duke University who’s pioneered methods to correlate levels of dust on people’s hands with levels found in their blood or urine. With two small children, a four-year-old son and a daughter who will be two next month, Stapleton said she thinks very carefully “as a mother and scientist” about the products she buys and washes her children’s hands frequently to reduce exposure. \u003c/p>\n\u003cp>She’s particularly worried about people using hand-me-down nursing pillows and other baby products that likely exude more flame retardants as they age. “No one to my knowledge is examining infants’ exposure to flame retardants from these small items,” she said. “They’re small but an infant spends a lot of contact time with them.” What’s more, babies are likely to go from sleep positioner to a car seat to a changing table, spending the better part of a day in contact with products that could be leaching the chemicals. \u003c/p>\n\u003cp>Last week at the flame retardant conference, researchers talked about the global reach of these chemicals, now detected in trees, sludge, wildlife and people around the world. They listed the wide range of health effects associated with the well-studied brominated flame retardants—including endocrine disruption and developmental, neurological and reproductive defects—and emphasized that the effects have been found in both animals and humans. They also reported worrying early results on new formulations like tetrabromobisphenol A (TBBPA), which is showing up in human breast milk and maternal cord blood samples.\u003c/p>\n\u003cp>Historically, TBBPA was added mostly to electronics and circuit boards in a “reactive mode,” which means it’s unlikely to leach from the product. But as Linda Birnbaum pointed out at the meeting, it’s now being used as a replacement for banned or discontinued brominated flame retardants in an “additive mode”—so it can offgas, migrate from the product into the air. “Which means more is going to get into the environment,” Birnbaum said, “which means more is going to get into people and wildlife.”\u003c/p>\n\u003cp>Birnbaum, director of the National Institute of Environmental Health Sciences and the National Toxicology Program, reported that a two-year study of TBBPA in rats and mice found a dose-related increase in aggressive uterine tumors in the female rats—“these are highly malignant tumors that metastasize to many different sites,” she told the crowd—as well as liver tumors in male and female mice. These results suggest, she said, that TBBPA is a “two species carcinogen” that warrants closer study.\u003c/p>\n\u003cp>A few months ago, Birnbaum told me that she used to think flame retardants were providing fire safety but now isn't so sure. She allows there may be applications that warrant them, like airplanes, but even then, she said, “If we think flame retardants are going to be helpful, why not use them in a reactive mode, so they don’t easily escape into the environment?”\u003c/p>\n\u003cp>A decade ago, after seeing data showing rising levels of flame retardants in people along with animal evidence linking neurological effects to exposure early in life, Birnbaum called attention to the issue with a paper called \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241790/pdf/ehp0112-000009.pdf\">\"Brominated Flame Retardants: Cause for Concern?\" \u003c/a>\u003c/p>\n\u003cp>Now, she said, “everything that is being seen in people when you look—and until recently, no one looked—is consistent with things that we’ve seen in animal models.”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The \u003ca href=\"http://www.bfr2013.com/upload/abstract-download/2013/BirnbaumPlenary.pdf\">weight of the evidence\u003c/a> inspired Birnbaum to write another paper. “I changed the question mark,” she said, “to an exclamation point.”\u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/2013/04/17/fire-safety-without-harm/fire/\" rel=\"attachment wp-att-52484\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2013/04/fire.jpg\" alt=\"fire\" width=\"640\" height=\"360\" class=\"alignleft size-full wp-image-52484\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2013/04/fire.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2013/04/fire-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003c/p>\n\u003cp>Last week, scientists and regulators from more than 20 countries gathered in San Francisco to discuss the latest research on flame retardants. \u003ca href=\"http://www.bfr2013.com/bfr2013_about.cfm\">The conference\u003c/a> lasted four days, but the theme of the meeting was clear from just a few talks: Do we need toxic chemicals to achieve fire safety?\u003c/p>\n\u003cp>For the past decade, scientists have voiced increasing concern about the potential health and environmental risks of these chemicals, which show up—and leach from—a growing number of consumer products. By now, most California consumers probably know that flame retardants permeate the foam in their couches and chairs, along with a surprising array of baby products. (On Monday, the \u003ca href=\"http://www.sfgate.com/health/article/Flame-retardants-to-be-removed-from-nap-mats-4436828.php\">San Francisco Chronicle noted\u003c/a> that at least some nap maps sold in the state will no longer contain flame retardants.)\u003c/p>\n\u003cp>As I reported yesterday in a \u003ca href=\"http://www.washingtonpost.com/national/health-science/flame-retardants-in-consumer-products-are-linked-to-health-and-cognitive-problems/2013/04/15/f5c7b2aa-8b34-11e2-9838-d62f083ba93f_story.html\">story for the Washington Post\u003c/a>, mounting evidence suggests that these brominated chemicals pose risks to human health. Californians carry among the highest levels of flame retardants in the world, which researchers attribute to a 70s-era flammability standard that requires foam products to resist an open flame for 12 seconds. Manufacturers typically used flame retardants to comply and many tailored their products to California’s standard—and considerable market share—to avoid double inventories. \u003c/p>\n\u003cp>Gov. Jerry Brown, concerned about the risks the chemicals pose to human health, \u003ca href=\"http://gov.ca.gov/news.php?id=17598\">called on the state agency\u003c/a> in charge of flammability standards to find a way to ensure fire safety without the need for toxic flame retardants. In March, the agency held \u003ca href=\"http://www.youtube.com/watch?v=_hOjKKdZR_s&feature=youtu.be\">a public hearing\u003c/a> on its new standard, revised to do just that. The new regulations go into effect July 2014.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Since 2011, when I started \u003ca href=\"http://www.environmentalhealthnews.org/ehs/news/2011/money-to-burn\">writing about flame retardants\u003c/a>, I’ve been struck by how the researchers studying these chemicals talk about their findings. Scientists tend to talk about their results in terms of what they don’t know and what new questions their studies raise. (All \u003ca href=\"http://www.scientificamerican.com/article.cfm?id=weak-link-fossil-darwinius\">exceptions duly noted\u003c/a>.) And those studying flame retardants do discuss their findings with all the usual caveats. But they also do something else. They tell me, \"We don’t like what we’re seeing.\" \u003c/p>\n\u003cp>A few weeks ago, I spoke with Heather Stapleton, a flame retardant expert at Duke University who’s pioneered methods to correlate levels of dust on people’s hands with levels found in their blood or urine. With two small children, a four-year-old son and a daughter who will be two next month, Stapleton said she thinks very carefully “as a mother and scientist” about the products she buys and washes her children’s hands frequently to reduce exposure. \u003c/p>\n\u003cp>She’s particularly worried about people using hand-me-down nursing pillows and other baby products that likely exude more flame retardants as they age. “No one to my knowledge is examining infants’ exposure to flame retardants from these small items,” she said. “They’re small but an infant spends a lot of contact time with them.” What’s more, babies are likely to go from sleep positioner to a car seat to a changing table, spending the better part of a day in contact with products that could be leaching the chemicals. \u003c/p>\n\u003cp>Last week at the flame retardant conference, researchers talked about the global reach of these chemicals, now detected in trees, sludge, wildlife and people around the world. They listed the wide range of health effects associated with the well-studied brominated flame retardants—including endocrine disruption and developmental, neurological and reproductive defects—and emphasized that the effects have been found in both animals and humans. They also reported worrying early results on new formulations like tetrabromobisphenol A (TBBPA), which is showing up in human breast milk and maternal cord blood samples.\u003c/p>\n\u003cp>Historically, TBBPA was added mostly to electronics and circuit boards in a “reactive mode,” which means it’s unlikely to leach from the product. But as Linda Birnbaum pointed out at the meeting, it’s now being used as a replacement for banned or discontinued brominated flame retardants in an “additive mode”—so it can offgas, migrate from the product into the air. “Which means more is going to get into the environment,” Birnbaum said, “which means more is going to get into people and wildlife.”\u003c/p>\n\u003cp>Birnbaum, director of the National Institute of Environmental Health Sciences and the National Toxicology Program, reported that a two-year study of TBBPA in rats and mice found a dose-related increase in aggressive uterine tumors in the female rats—“these are highly malignant tumors that metastasize to many different sites,” she told the crowd—as well as liver tumors in male and female mice. These results suggest, she said, that TBBPA is a “two species carcinogen” that warrants closer study.\u003c/p>\n\u003cp>A few months ago, Birnbaum told me that she used to think flame retardants were providing fire safety but now isn't so sure. She allows there may be applications that warrant them, like airplanes, but even then, she said, “If we think flame retardants are going to be helpful, why not use them in a reactive mode, so they don’t easily escape into the environment?”\u003c/p>\n\u003cp>A decade ago, after seeing data showing rising levels of flame retardants in people along with animal evidence linking neurological effects to exposure early in life, Birnbaum called attention to the issue with a paper called \u003ca href=\"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1241790/pdf/ehp0112-000009.pdf\">\"Brominated Flame Retardants: Cause for Concern?\" \u003c/a>\u003c/p>\n\u003cp>Now, she said, “everything that is being seen in people when you look—and until recently, no one looked—is consistent with things that we’ve seen in animal models.”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>The \u003ca href=\"http://www.bfr2013.com/upload/abstract-download/2013/BirnbaumPlenary.pdf\">weight of the evidence\u003c/a> inspired Birnbaum to write another paper. “I changed the question mark,” she said, “to an exclamation point.”\u003c/p>\n\n\u003c/div>\u003c/p>",
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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",
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