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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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"content": "\u003cp>Like all mammals, the Neanderthals breast-fed their babies. Scientists wanted to know: For how long? \u003c/p>\n\u003cp>Today in \u003ca href=\"http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12169.html\">Nature\u003c/a>, a team of researchers, including several from UC Berkeley, say they’ve answered that question by looking at the fossilized tooth of an eight-year old Neanderthal child, discovered in a Belgian cave.\u003c/p>\n\u003cp>Asa Bradman is an environmental health scientist at UC Berkeley and a co-author on the paper. He says teeth are like a time capsule. \u003c/p>\n\u003cp>“Because teeth grow in rings, kind of like trees do, you can actually date when a given layer of the tooth was put down.”\u003c/p>\n\u003cp>Breast milk is high in barium, which crystalizes in teeth, even before they emerge from a baby’s gum line. \u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Bradman, UC Berkeley’s Brenda Eskenazi, and others on the team hypothesized that if they could learn how barium deposits correspond with age, they might reveal the breast-feeding histories of our distant cousins the Neanderthals, who roamed Europe 30,000 to 300,000 years ago. \u003c/p>\n\u003cp>But first, they had to establish that their methodology worked. So, they tried it out with humans: a group of pregnant women recruited in Salinas, California as part of the \u003ca href=\"http://cerch.org/research-programs/chamacos/\">Health Assessment of Mothers and Children Study\u003c/a>. \u003c/p>\n\u003cp>Twice during pregnancy and at six-month intervals after birth, researchers asked the mothers whether they were using breast milk or formula, and noted the age at which mothers introduced food to their children. \u003c/p>\n\u003cfigure id=\"attachment_3214\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/NBF_Nature_cropped.jpg\" rel=\"attachment wp-att-3214\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/NBF_Nature_cropped.jpg\" alt=\"Analysis of a Neanderthal tooth, showing Barium levels. (Photo courtesy Nature)\" width=\"640\" height=\"582\" class=\"size-full wp-image-3214\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Analysis of a Neanderthal tooth, showing Barium levels. (Photo courtesy Nature)\u003c/figcaption>\u003c/figure>\n\u003cp>Years later, when the kids started to lose their teeth, researchers brought those teeth in for lab analysis, to see how barium levels corresponded to breast feeding histories. \u003c/p>\n\u003cp>They did the same thing with macaque monkeys living at UC Davis. \u003c/p>\n\u003cp>Analysis of both species showed a clear breakdown of when barium levels were highest – i.e, during periods of exclusive breast feeding – and when they returned to “baseline” levels, after the child had weaned. \u003c/p>\n\u003cp>“In the tooth,” says Bradman, “we can actually see a fingerprint, so to speak, of the milk intake during the life of the child.”\u003c/p>\n\u003cp>In Australia, a team of scientists analyzed the fossilized tooth of an eight-year old Neanderthal child, some 100 thousand years old, found in Belgium’s Scladina cave. \u003c/p>\n\u003cp>“The child was exclusively breastfed for about seven months and then continued to breastfeed up until 14 months,” says Bradman.\u003c/p>\n\u003cp>“It’s remarkably similar to the recommendations by the American Academy of Pediatrics for modern humans.”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>For more on this story, See Adam Cole’s excellent \u003ca href=\"http://www.npr.org/blogs/health/2013/05/21/185813855/Scientific-Tooth-Fairies-Investigate-Neanderthal-Breastfeeding\">article\u003c/a> on npr.org. \u003c/p>\n\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Bradman, UC Berkeley’s Brenda Eskenazi, and others on the team hypothesized that if they could learn how barium deposits correspond with age, they might reveal the breast-feeding histories of our distant cousins the Neanderthals, who roamed Europe 30,000 to 300,000 years ago. \u003c/p>\n\u003cp>But first, they had to establish that their methodology worked. So, they tried it out with humans: a group of pregnant women recruited in Salinas, California as part of the \u003ca href=\"http://cerch.org/research-programs/chamacos/\">Health Assessment of Mothers and Children Study\u003c/a>. \u003c/p>\n\u003cp>Twice during pregnancy and at six-month intervals after birth, researchers asked the mothers whether they were using breast milk or formula, and noted the age at which mothers introduced food to their children. \u003c/p>\n\u003cfigure id=\"attachment_3214\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/NBF_Nature_cropped.jpg\" rel=\"attachment wp-att-3214\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/NBF_Nature_cropped.jpg\" alt=\"Analysis of a Neanderthal tooth, showing Barium levels. (Photo courtesy Nature)\" width=\"640\" height=\"582\" class=\"size-full wp-image-3214\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Analysis of a Neanderthal tooth, showing Barium levels. (Photo courtesy Nature)\u003c/figcaption>\u003c/figure>\n\u003cp>Years later, when the kids started to lose their teeth, researchers brought those teeth in for lab analysis, to see how barium levels corresponded to breast feeding histories. \u003c/p>\n\u003cp>They did the same thing with macaque monkeys living at UC Davis. \u003c/p>\n\u003cp>Analysis of both species showed a clear breakdown of when barium levels were highest – i.e, during periods of exclusive breast feeding – and when they returned to “baseline” levels, after the child had weaned. \u003c/p>\n\u003cp>“In the tooth,” says Bradman, “we can actually see a fingerprint, so to speak, of the milk intake during the life of the child.”\u003c/p>\n\u003cp>In Australia, a team of scientists analyzed the fossilized tooth of an eight-year old Neanderthal child, some 100 thousand years old, found in Belgium’s Scladina cave. \u003c/p>\n\u003cp>“The child was exclusively breastfed for about seven months and then continued to breastfeed up until 14 months,” says Bradman.\u003c/p>\n\u003cp>“It’s remarkably similar to the recommendations by the American Academy of Pediatrics for modern humans.”\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>For more on this story, See Adam Cole’s excellent \u003ca href=\"http://www.npr.org/blogs/health/2013/05/21/185813855/Scientific-Tooth-Fairies-Investigate-Neanderthal-Breastfeeding\">article\u003c/a> on npr.org. \u003c/p>\n\n\u003c/div>\u003c/p>",
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"content": "\u003cp>Journalist Jon Mooallem noticed that his young daughter was always surrounded by wild animals: butterflies on her pajamas, a stuffed toy owl, and beavers in her bedtime stories. But these romantic portrayals, he says, hid a harsh reality. Scientists estimate half of all species could be gone by the turn of the century. So he embarked on his own journey to track down three endangered animals, and discovered the extreme — even futile — lengths humans go to save them. Jon Mooallem discusses his book, “Wild Ones,” and the complex intersections of man and nature. \u003ca href=\"http://www.kqed.org/epArchive/R201305201000?pid=RD19\" target=\"_blank\" rel=\"noopener\">»\u003c/a> \u003c/p>\n\u003cp>Source: \u003ca href=\"http://www.kqed.org/epArchive/R201305201000?pid=RD19\" target=\"_blank\" title=\"Jon Mooallem on the Weird World of People and Animals\" rel=\"noopener\">Forum – Science\u003c/a>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\u003cp>\u003c/p>\n",
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"content": "\u003cp>A new edition of the most widely used psychiatric guide to mental disorders — “The Diagnostic and Statistical Manual of Mental Disorders” — was released this past weekend in San Francisco at a meeting of the American Psychiatric Association. The manual has a big impact on public health, including what insurance companies will cover, the drugs that regulators will approve, and even which children will receive special education services. But critics say that the manual is outdated and question the validity of several new diagnoses. \u003ca href=\"http://www.kqed.org/epArchive/R201305200900?pid=RD19\" target=\"_blank\" rel=\"noopener\">»\u003c/a> \u003c/p>\n\u003cp>Source: \u003ca href=\"http://www.kqed.org/epArchive/R201305200900?pid=RD19\" target=\"_blank\" title=\"Revised Manual of Mental Disorders Stirs Controversy\" rel=\"noopener\">Forum – Science\u003c/a>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\u003cp>\u003c/p>\n",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp>A new edition of the most widely used psychiatric guide to mental disorders — “The Diagnostic and Statistical Manual of Mental Disorders” — was released this past weekend in San Francisco at a meeting of the American Psychiatric Association. The manual has a big impact on public health, including what insurance companies will cover, the drugs that regulators will approve, and even which children will receive special education services. But critics say that the manual is outdated and question the validity of several new diagnoses. \u003ca href=\"http://www.kqed.org/epArchive/R201305200900?pid=RD19\" target=\"_blank\" rel=\"noopener\">»\u003c/a> \u003c/p>\n\u003cp>Source: \u003ca href=\"http://www.kqed.org/epArchive/R201305200900?pid=RD19\" target=\"_blank\" title=\"Revised Manual of Mental Disorders Stirs Controversy\" rel=\"noopener\">Forum – Science\u003c/a>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"disqusTitle": "Saved From Living Death: How Genetically Modifying Chestnuts Could Bring Them Back",
"title": "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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"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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"title": "Smartphone Apps Enable a New Phenomenon: the Grassroots 'Bio-blitz'",
"headTitle": "Smartphone Apps Enable a New Phenomenon: the Grassroots ‘Bio-blitz’ | KQED",
"content": "\u003cp> \u003c/p>\n\u003cp>On a sunny day in May when 60 people canvassed San Francisco’s \u003ca href=\"https://maps.google.com/maps?q=mclaren+park&ll=37.721883,-122.420526&spn=0.009522,0.01929&fb=1&gl=us&hq=mclaren+park&hnear=0x80857d8b28aaed03:0x71b415d535759367,Oakland,+CA&cid=0,0,15376763166238386291&t=h&z=16&iwloc=A\" target=\"_blank\" rel=\"noopener\">McLaren Park\u003c/a> and logged sightings of more than 200 species of plants and animals in just three hours, it seemed like a coming-of-age for smartphone-powered citizen science: At this point, just about anyone can do it and produce a remarkable quantity of usable data.\u003c/p>\n\u003cp>Traditional bioblitzes often include scientists intensively collecting specimens over a 24-hour period. That takes special equipment and, depending on the species and the park, special permits. A smartphone-powered bioblitz skips the specimens in favor of map coordinates and photos. Without the need for permits or special nets and traps, the McLaren Park Urban Bioblitz could be almost entirely grassroots, fueled by two all-volunteer groups, \u003ca href=\"http://nerdsfornature.org\" target=\"_blank\" rel=\"noopener\">Nerds for Nature\u003c/a> (which I helped found) and \u003ca href=\"http://savemclarenpark.org\" target=\"_blank\" rel=\"noopener\">Save McLaren Park\u003c/a>, with major assists from \u003ca href=\"http://inaturalist.org\" target=\"_blank\" rel=\"noopener\">iNaturalist.org\u003c/a> and \u003ca href=\"http://baynature.org\" target=\"_blank\" rel=\"noopener\">Bay Nature Institute\u003c/a>.\u003c/p>\n\u003cp>“In terms of research on biodiversity and biogeography, like distribution of bird species, this data is extremely valuable,” said Scott Loarie, iNaturalist’s codirector and a research fellow at Stanford. Before the blitz, Loarie had checked existing museum records for biological specimens collected at McLaren park and found almost none. “We were able to gather orders of magnitude more observations in just a few hours compared to 25 specimens in the history of collecting.”\u003c/p>\n\u003cp>Using iNaturalist’s mobile app, the group flew through the 300-acre park in three hours and racked up more than 1,250 sightings. The near ubiquity of smartphones is what makes an event like this possible: Just about everyone is walking around with a device capable of things that, a decade ago, would have been the purview of professionals with an armload of gadgets, and people are so comfortable using map and photo apps that there’s almost no training required. (Correctly identifying species is another matter, but luckily iNaturalist has a good online community that helps out with that.)\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>“When the city developed the [San Francisco] \u003ca href=\"http://proceedings.esri.com/library/userconf/proc01/professional/papers/pap408/p408.htm\" target=\"_blank\" rel=\"noopener\">Natural Areas Plan\u003c/a> back in the 90s, there was this huge project to get all these professionals mapping out all this stuff,” said Ken McGary, a leader of Save McLaren Park who lives nearby. “Now 15 or 20 years later, we did something similar with a few experts and volunteers. And we’re also inspiring a new group of naturalists.”\u003c/p>\n\u003cp>Now, according to Jean Farrington, director of lifelong learning at the California Academy of Sciences, the academy hopes to use the McLaren Bioblitz as a model for a series of bioblitzes, partnering with groups like Nerds for Nature, Bay Nature, and local park groups to document species across San Francisco as part of an upcoming San Francisco biodiversity citizen science campaign.\u003c/p>\n\u003cfigure id=\"attachment_2751\" class=\"wp-caption alignright\" style=\"max-width: 243px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2751\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Ueda-8730190853_3780c0c890_b-243x162.jpg\" alt=\"umber skippers, Ken-ichi Ueda, creative commons\" width=\"243\" height=\"162\">\u003cfigcaption class=\"wp-caption-text\">umber skippers, photo by Ken-ichi Ueda, creative commons\u003c/figcaption>\u003c/figure>\n\u003cp>iNaturalist was the brainchild of Ken-ichi Ueda: He and other students at UC Berkeley created it for a masters project in 2008. Since then, as KQED has reported in the past, it’s gotten bigger and better. iNat users are \u003ca href=\"http://science.kqed.org/quest/audio/counting-climate-challenged-pikas/\" target=\"_blank\" rel=\"noopener\">tracking pikas in the High Sierra\u003c/a>, \u003ca href=\"http://blogs.kqed.org/climatewatch/2011/09/27/snapping-snakes-for-science-with-your-iphone/#more-15211\" target=\"_blank\" rel=\"noopener\">logging global amphibian sightings\u003c/a>, and \u003ca href=\"http://www.californiareport.org/archive/R201103041630/b\" target=\"_blank\" rel=\"noopener\">chronicling the effects of climate change at Stanford’s Jasper Ridge\u003c/a>.\u003c/p>\n\u003cp>But this was the first time Ueda and Loarie helped organize an on-the-ground blitz. None of us knew if turning novices loose on the park with minimal guidance would work. It did. “You don’t need to know what you’re looking at, but you can still record interesting and scientifically relevant data,” said Ueda. “The one pipevine swallowtail was recorded by a guy who just showed up and wasn’t looking for it.”\u003c/p>\n\u003cp>We divided up into four teams and fanned out across the park, trying to find as many different kinds of plants and animals as we could in just three hours, and recording our sightings using the iNaturalist smartphone app. Blitzers found the expected—like \u003ca href=\"http://www.inaturalist.org/observations/265823\" target=\"_blank\" rel=\"noopener\">a raven\u003c/a> or \u003ca href=\"http://www.inaturalist.org/observations/265821\" target=\"_blank\" rel=\"noopener\">a scrub jay\u003c/a>—but also the unexpected, like that \u003ca href=\"http://www.inaturalist.org/observations/265814\" target=\"_blank\" rel=\"noopener\">pipevine swallowtail butterfly\u003c/a>, a \u003ca href=\"http://www.inaturalist.org/observations/263795\" target=\"_blank\" rel=\"noopener\">Lazuli bunting\u003c/a> and oddest of all, a \u003ca href=\"http://www.inaturalist.org/observations/265651\" target=\"_blank\" rel=\"noopener\">dead Anna’s hummingbird resting in a cala lily\u003c/a>.\u003c/p>\n\u003cfigure id=\"attachment_2748\" class=\"wp-caption alignnone\" style=\"max-width: 900px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-2748\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Schwarz-DSC00074.jpg\" alt=\"Logging a plant with giant leaves. Photo by Tamara Schwarz\" width=\"900\" height=\"600\">\u003cfigcaption class=\"wp-caption-text\">One team was fascinated by this South American import (genus Gunnera) with enormous leaves and spiny stalks. Photo by Tamara Schwarz.\u003c/figcaption>\u003c/figure>\n\u003cp>And people had a lot of fun making those discoveries: “I guess it was pretty obvious that we were having a good time,” said one blitzer, “because a woman who happened to be jogging through the park stopped me to ask what group we were with and how she can join.” At the end of the day, we watched as the numbers rolled in on iNaturalist’s \u003ca href=\"http://www.inaturalist.org/observations/stats?place_id=mclaren-park-san-francisco-ca-us&d1=2013-05-11&d2=2013-05-12\" target=\"_blank\" rel=\"noopener\">leaderboard page\u003c/a>. Once those sightings have confirmed species IDs, the data flows to both the \u003ca href=\"http://gbif.org\" target=\"_blank\" rel=\"noopener\">Global Biodiversity Information Facility\u003c/a> (GBIF) and the \u003ca href=\"http://eol.org\" target=\"_blank\" rel=\"noopener\">Encyclopedia of Life\u003c/a>, where researchers all over the world can make use of it. Loarie tells me that some 66,000 verified research-grade observations are now in the GBIF database (out of more than 200,000 total sightings on iNat).\u003c/p>\n\u003cfigure id=\"attachment_2750\" class=\"wp-caption alignright\" style=\"max-width: 243px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2750\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Schwarz-DSC00109-243x162.jpg\" alt=\"Blitzers at McLaren Park, photo by Tamara Schwarz\" width=\"243\" height=\"162\">\u003cfigcaption class=\"wp-caption-text\">Blitzers at McLaren Park, photo by Tamara Schwarz\u003c/figcaption>\u003c/figure>\n\u003cp>iNaturalist data can be used not just for academic research, but for grassroots restoration and outreach as well. On Saturday, we heard about an SF State student using iNaturalist data for research on Pacific chorus frogs. Local activists concerned about \u003ca href=\"http://blog.sfgate.com/cityinsider/2013/05/02/deadheads-fight-potential-renaming-of-jerry-garcia-amphitheater/\" target=\"_blank\" rel=\"noopener\">a new plan for the Jerry Garcia Amphitheater\u003c/a> want to log wildlife in that area. Amber Hasselbring, director of \u003ca href=\"http://natureinthecity.org\" target=\"_blank\" rel=\"noopener\">Nature in the City\u003c/a>, and lepidopterist \u003ca href=\"http://sfbutterfly.com\" target=\"_blank\" rel=\"noopener\">Liam O’Brien\u003c/a> are using the app to \u003ca href=\"http://baynature.org/articles/whats-a-tiger-swallowtail-doing-in-downtown-san-francisco/\" target=\"_blank\" rel=\"noopener\">track butterflies on Market Street\u003c/a>.\u003c/p>\n\u003cp>Beyond all those specific cases, I love just looking at the cast of characters we know live in a park once it’s gotten the attention of iNaturalist users. Here’s \u003ca href=\"http://www.inaturalist.org/places/mclaren-park-san-francisco-ca-us\" target=\"_blank\" rel=\"noopener\">McLaren Park’s iNaturalist page\u003c/a>. Who wouldn’t want to go there?\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>Thanks to Tony Iwane for producing the event video, and to Ken McGary, Tom Scott, Ken-ichi Ueda, Scott Loarie, Ryan Kaldari, Liam O’Brien, and many others for making the event possible.\u003c/em>\u003c/p>\n\n",
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"excerpt": "Traditional bioblitzes often include scientists intensively collecting specimens over a 24-hour period. That takes special equipment and, depending on the species and the park, special permits. But with help from smartphones, just about anyone can produce a remarkable quantity of usable data.",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cp> \u003c/p>\n\u003cp>On a sunny day in May when 60 people canvassed San Francisco’s \u003ca href=\"https://maps.google.com/maps?q=mclaren+park&ll=37.721883,-122.420526&spn=0.009522,0.01929&fb=1&gl=us&hq=mclaren+park&hnear=0x80857d8b28aaed03:0x71b415d535759367,Oakland,+CA&cid=0,0,15376763166238386291&t=h&z=16&iwloc=A\" target=\"_blank\" rel=\"noopener\">McLaren Park\u003c/a> and logged sightings of more than 200 species of plants and animals in just three hours, it seemed like a coming-of-age for smartphone-powered citizen science: At this point, just about anyone can do it and produce a remarkable quantity of usable data.\u003c/p>\n\u003cp>Traditional bioblitzes often include scientists intensively collecting specimens over a 24-hour period. That takes special equipment and, depending on the species and the park, special permits. A smartphone-powered bioblitz skips the specimens in favor of map coordinates and photos. Without the need for permits or special nets and traps, the McLaren Park Urban Bioblitz could be almost entirely grassroots, fueled by two all-volunteer groups, \u003ca href=\"http://nerdsfornature.org\" target=\"_blank\" rel=\"noopener\">Nerds for Nature\u003c/a> (which I helped found) and \u003ca href=\"http://savemclarenpark.org\" target=\"_blank\" rel=\"noopener\">Save McLaren Park\u003c/a>, with major assists from \u003ca href=\"http://inaturalist.org\" target=\"_blank\" rel=\"noopener\">iNaturalist.org\u003c/a> and \u003ca href=\"http://baynature.org\" target=\"_blank\" rel=\"noopener\">Bay Nature Institute\u003c/a>.\u003c/p>\n\u003cp>“In terms of research on biodiversity and biogeography, like distribution of bird species, this data is extremely valuable,” said Scott Loarie, iNaturalist’s codirector and a research fellow at Stanford. Before the blitz, Loarie had checked existing museum records for biological specimens collected at McLaren park and found almost none. “We were able to gather orders of magnitude more observations in just a few hours compared to 25 specimens in the history of collecting.”\u003c/p>\n\u003cp>Using iNaturalist’s mobile app, the group flew through the 300-acre park in three hours and racked up more than 1,250 sightings. The near ubiquity of smartphones is what makes an event like this possible: Just about everyone is walking around with a device capable of things that, a decade ago, would have been the purview of professionals with an armload of gadgets, and people are so comfortable using map and photo apps that there’s almost no training required. (Correctly identifying species is another matter, but luckily iNaturalist has a good online community that helps out with that.)\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“When the city developed the [San Francisco] \u003ca href=\"http://proceedings.esri.com/library/userconf/proc01/professional/papers/pap408/p408.htm\" target=\"_blank\" rel=\"noopener\">Natural Areas Plan\u003c/a> back in the 90s, there was this huge project to get all these professionals mapping out all this stuff,” said Ken McGary, a leader of Save McLaren Park who lives nearby. “Now 15 or 20 years later, we did something similar with a few experts and volunteers. And we’re also inspiring a new group of naturalists.”\u003c/p>\n\u003cp>Now, according to Jean Farrington, director of lifelong learning at the California Academy of Sciences, the academy hopes to use the McLaren Bioblitz as a model for a series of bioblitzes, partnering with groups like Nerds for Nature, Bay Nature, and local park groups to document species across San Francisco as part of an upcoming San Francisco biodiversity citizen science campaign.\u003c/p>\n\u003cfigure id=\"attachment_2751\" class=\"wp-caption alignright\" style=\"max-width: 243px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2751\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Ueda-8730190853_3780c0c890_b-243x162.jpg\" alt=\"umber skippers, Ken-ichi Ueda, creative commons\" width=\"243\" height=\"162\">\u003cfigcaption class=\"wp-caption-text\">umber skippers, photo by Ken-ichi Ueda, creative commons\u003c/figcaption>\u003c/figure>\n\u003cp>iNaturalist was the brainchild of Ken-ichi Ueda: He and other students at UC Berkeley created it for a masters project in 2008. Since then, as KQED has reported in the past, it’s gotten bigger and better. iNat users are \u003ca href=\"http://science.kqed.org/quest/audio/counting-climate-challenged-pikas/\" target=\"_blank\" rel=\"noopener\">tracking pikas in the High Sierra\u003c/a>, \u003ca href=\"http://blogs.kqed.org/climatewatch/2011/09/27/snapping-snakes-for-science-with-your-iphone/#more-15211\" target=\"_blank\" rel=\"noopener\">logging global amphibian sightings\u003c/a>, and \u003ca href=\"http://www.californiareport.org/archive/R201103041630/b\" target=\"_blank\" rel=\"noopener\">chronicling the effects of climate change at Stanford’s Jasper Ridge\u003c/a>.\u003c/p>\n\u003cp>But this was the first time Ueda and Loarie helped organize an on-the-ground blitz. None of us knew if turning novices loose on the park with minimal guidance would work. It did. “You don’t need to know what you’re looking at, but you can still record interesting and scientifically relevant data,” said Ueda. “The one pipevine swallowtail was recorded by a guy who just showed up and wasn’t looking for it.”\u003c/p>\n\u003cp>We divided up into four teams and fanned out across the park, trying to find as many different kinds of plants and animals as we could in just three hours, and recording our sightings using the iNaturalist smartphone app. Blitzers found the expected—like \u003ca href=\"http://www.inaturalist.org/observations/265823\" target=\"_blank\" rel=\"noopener\">a raven\u003c/a> or \u003ca href=\"http://www.inaturalist.org/observations/265821\" target=\"_blank\" rel=\"noopener\">a scrub jay\u003c/a>—but also the unexpected, like that \u003ca href=\"http://www.inaturalist.org/observations/265814\" target=\"_blank\" rel=\"noopener\">pipevine swallowtail butterfly\u003c/a>, a \u003ca href=\"http://www.inaturalist.org/observations/263795\" target=\"_blank\" rel=\"noopener\">Lazuli bunting\u003c/a> and oddest of all, a \u003ca href=\"http://www.inaturalist.org/observations/265651\" target=\"_blank\" rel=\"noopener\">dead Anna’s hummingbird resting in a cala lily\u003c/a>.\u003c/p>\n\u003cfigure id=\"attachment_2748\" class=\"wp-caption alignnone\" style=\"max-width: 900px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-2748\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Schwarz-DSC00074.jpg\" alt=\"Logging a plant with giant leaves. Photo by Tamara Schwarz\" width=\"900\" height=\"600\">\u003cfigcaption class=\"wp-caption-text\">One team was fascinated by this South American import (genus Gunnera) with enormous leaves and spiny stalks. Photo by Tamara Schwarz.\u003c/figcaption>\u003c/figure>\n\u003cp>And people had a lot of fun making those discoveries: “I guess it was pretty obvious that we were having a good time,” said one blitzer, “because a woman who happened to be jogging through the park stopped me to ask what group we were with and how she can join.” At the end of the day, we watched as the numbers rolled in on iNaturalist’s \u003ca href=\"http://www.inaturalist.org/observations/stats?place_id=mclaren-park-san-francisco-ca-us&d1=2013-05-11&d2=2013-05-12\" target=\"_blank\" rel=\"noopener\">leaderboard page\u003c/a>. Once those sightings have confirmed species IDs, the data flows to both the \u003ca href=\"http://gbif.org\" target=\"_blank\" rel=\"noopener\">Global Biodiversity Information Facility\u003c/a> (GBIF) and the \u003ca href=\"http://eol.org\" target=\"_blank\" rel=\"noopener\">Encyclopedia of Life\u003c/a>, where researchers all over the world can make use of it. Loarie tells me that some 66,000 verified research-grade observations are now in the GBIF database (out of more than 200,000 total sightings on iNat).\u003c/p>\n\u003cfigure id=\"attachment_2750\" class=\"wp-caption alignright\" style=\"max-width: 243px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-2750\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/Schwarz-DSC00109-243x162.jpg\" alt=\"Blitzers at McLaren Park, photo by Tamara Schwarz\" width=\"243\" height=\"162\">\u003cfigcaption class=\"wp-caption-text\">Blitzers at McLaren Park, photo by Tamara Schwarz\u003c/figcaption>\u003c/figure>\n\u003cp>iNaturalist data can be used not just for academic research, but for grassroots restoration and outreach as well. On Saturday, we heard about an SF State student using iNaturalist data for research on Pacific chorus frogs. Local activists concerned about \u003ca href=\"http://blog.sfgate.com/cityinsider/2013/05/02/deadheads-fight-potential-renaming-of-jerry-garcia-amphitheater/\" target=\"_blank\" rel=\"noopener\">a new plan for the Jerry Garcia Amphitheater\u003c/a> want to log wildlife in that area. Amber Hasselbring, director of \u003ca href=\"http://natureinthecity.org\" target=\"_blank\" rel=\"noopener\">Nature in the City\u003c/a>, and lepidopterist \u003ca href=\"http://sfbutterfly.com\" target=\"_blank\" rel=\"noopener\">Liam O’Brien\u003c/a> are using the app to \u003ca href=\"http://baynature.org/articles/whats-a-tiger-swallowtail-doing-in-downtown-san-francisco/\" target=\"_blank\" rel=\"noopener\">track butterflies on Market Street\u003c/a>.\u003c/p>\n\u003cp>Beyond all those specific cases, I love just looking at the cast of characters we know live in a park once it’s gotten the attention of iNaturalist users. Here’s \u003ca href=\"http://www.inaturalist.org/places/mclaren-park-san-francisco-ca-us\" target=\"_blank\" rel=\"noopener\">McLaren Park’s iNaturalist page\u003c/a>. Who wouldn’t want to go there?\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003cem>Thanks to Tony Iwane for producing the event video, and to Ken McGary, Tom Scott, Ken-ichi Ueda, Scott Loarie, Ryan Kaldari, Liam O’Brien, and many others for making the event possible.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>",
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"title": "A Mind for Animals: An Interview with Virginia Morell",
"headTitle": "A Mind for Animals: An Interview with Virginia Morell | KQED",
"content": "\u003cfigure id=\"attachment_2716\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/chimp.jpg\" rel=\"attachment wp-att-2716\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/chimp.jpg\" alt=\"Young male chimp (Credit: Frans de Waal/Emory University)\" width=\"640\" height=\"360\" class=\"size-full wp-image-2716\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Young male chimp (Credit: Frans de Waal/Emory University)\u003c/figcaption>\u003c/figure>\n\u003cp>When I was little, I often consulted our family cat, Scoots, about how we might spend the day. I don’t remember when I realized my parents were teasing me when they asked what he thought of my suggestions, but I do remember wishing there was a way for them to join our conversations. Of course, I didn’t realize it at the time, the mid-1960s, but my parents’ view of animal minds, or the lack thereof, sat squarely within that of mainstream science—which remained stubbornly stagnant on this point for decades. \u003c/p>\n\u003cp>Science’s slow recognition of the rich inner lives of animals is a subject that has long fascinated \u003ca href=\"http://www.gillianmackenzieagency.com/books/authors/48\">Virginia Morell\u003c/a>, a frequent contributor to \u003cem>National Geographic\u003c/em> and \u003cem>Science\u003c/em> and author of the new book \u003ca href=\"http://gillianmackenzieagency.com/books/48\">Animal Wise\u003c/a>. One of the stories that laid the conceptual foundation for her book, \u003ca href=\"http://ngm.nationalgeographic.com/2008/03/animal-minds/virginia-morell-text\">“Minds of Their Own,”\u003c/a> was largely responsible for an all-time best-selling issue for \u003cem>National Geographic\u003c/em>. Morell thinks it resonated with readers, who finally got a chance to see that scientists—not just crazy animal lovers—believe that animals think. \u003c/p>\n\u003cp>Morell will read from Animal Wise at \u003ca href=\"http://bookpassage.com/event/virginia-morell-animal-wise\">Book Passage\u003c/a> in Corte Madera, May 15 at 7 p.m. I spoke with her last month.\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> What inspired you to write this book?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> It was a logical spinoff after doing the \u003ca href=\"https://www.kirkusreviews.com/book-reviews/virginia-morell/ancestral-passions/\">book about the Leakeys\u003c/a>, which explored our fossil ancestry. Then, after seeing chimpanzees in the wild, there were just so many clearcut moments you saw our shared ancestry. My husband and I would come back to the visitors’ guest house where we were staying and describe what we’d seen and we’d talk about people, and then we’d say, I mean chimpanzees. And that fascinated me. Then having my own dog made me interested in these issues. So I began to write about the discoveries that scientists were making about what animals do, both in the wild and in the lab, and you could feel the chipping away of the old standard that everything was a response to a stimulus.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>And it puzzled me because, it’s having that evolutionary perspective that makes you wonder, well, if everything’s a response to a stimulus in human animals, what’s changed, how did this dramatic change come about. Why are we unique, why are we special? The focus originally even among people who wanted to understand that cognitive shift was solely on what chimpanzees or other great apes were like, sometimes maybe monkeys, but always on the primate mind. And then as discoveries began to come out of other fields and other animals that people were looking at, you could see that there were more similarities out there than there were differences. \u003c/p>\n\u003cp>I began to wonder what the scientists themselves felt about their discoveries and I wanted to show how we know these things. How do you get around the problem of not being able to ask an animal. When journalists report on the latest science news, we rarely talk about who the animals are and who the researchers are, what drew them to studying their animals. I was quite interested in that too. I always wondered who are the rats who are pressing the levers. Who are these pigeons? What draws a person to [study] that? Surely it’s more than wanting to see the animals as stimulus-response machines.\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> Some of the scientists in your book are pushing the boundaries of what we know about animal cognition. How did you deal with ideas that other scientists might consider “fringe”?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> In the case of \u003ca href=\"http://bio.psu.edu/directory/vab12\">Victoria Braithwaite\u003c/a> (whose studies suggest fish feel pain), there have been challenges to her studies, that’s true. But the question for me was how would I deal with it? Would I do a he said/she said kind of a book, which can be very boring and insider baseball. Or was I going to let these scientists present their side of things and add this to the public debate? And that’s what I chose to do. Certainly her team’s studies were published in high-profile journals, and I was also struck by the comparative study she did, where she showed the fish that were injected with the bee venom versus those that had the saline injection, and the fish with the bee venom changed their behavior. Those fish were adversely affected whereas those with the saline injections were not. To me, that spoke volumes.\u003c/p>\n\u003cfigure id=\"attachment_2713\" class=\"wp-caption alignleft\" style=\"max-width: 240px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/rsz_virginia_morell_credit_michael_mcrae_high_res.jpg\" rel=\"attachment wp-att-2713\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/rsz_virginia_morell_credit_michael_mcrae_high_res.jpg\" alt=\"Virginia Morell and her dog, Buckaroo\" width=\"240\" height=\"312\" class=\"size-full wp-image-2713\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Virginia Morell and her dog, Buckaroo\u003c/figcaption>\u003c/figure>\n\u003cp>In \u003ca href=\"http://www.brandeis.edu/facultyguide/person.html?emplid=2d3923e829d95e3849ac8001f5c5fa254b5cf400\">Irene Pepperberg’s\u003c/a> case I think she was hamstrung from the beginning. A lot of the questions she was faced with at the beginning we know now were not valid questions because birds have all the key parts of their brain for doing the type of cognitive tasks that Alex [\u003ca href=\"http://www.youtube.com/watch?v=vXoTaZotdHg\">the famed African gray parrot\u003c/a>] was capable of doing. When she first started, it was thought that they lacked some key neural anatomy. Now we know Alex had the mental equipment, the basic biology needed to do the sort of abstract thinking he was doing and that he’s a lifelong vocal learner as we are. \u003c/p>\n\u003cp>I was also struck by the fact that most of the younger scientists, such as \u003ca href=\"http://www.nbb.cornell.edu/berg.shtml\">Karl Berg\u003c/a> and other bird researchers that I’ve spoken to, very much respect Irene’s work. It’s a generational change. I was hesitant when I first started the [National] Geographic story when people asked if I was going to go see Koko and Alex, and I thought, “I don’t know. Those are kind of tainted studies.” And then\u003ca href=\"http://www.zoo.ox.ac.uk/people/view/kacelnik_a.htm\"> Alex Kacelnik\u003c/a> said, “My God, you’ve got to. This is the only animal in the world that’s going to open its mouth and speak to you. And in English!”\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> Were there any behaviors or discoveries the scientists told you about that really surprised you?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> I think with every single animal I had that experience. Take the ants. When you saw the size of them, any ant is minuscule but with these, you had to have a magnifying glass to see them, and they were making these amazing decisions. They can go into a crack, they can measure the size of a space and know how large a space they want and how high the ceiling needs to be, how many entrances. They have all these different ways to judge the different requirements they have for just the size of their homes, let alone all the other things they do in their lives. That astonished me. \u003c/p>\n\u003cp>And the fish being able to watch and copy another’s behavior, almost immediately. That requires the fish, the \u003ca href=\"http://www.youtube.com/watch?v=fhBZ40jIo4Q\">archerfish\u003c/a>, to put themselves in the position of the other fish that’s shooting, to make that shot themselves. \u003c/p>\n\u003cp>And Alex was a puzzle. I try and think how on earth a bird would spend its life for Irene, practicing. And the attention to detail that the elephants have, these big animals the size of ships moving across the landscape, they’re paying attention to everything. \u003ca href=\"http://www.wildforlifefoundation.org/joycepoole.html\">Joyce Poole\u003c/a> told me one time she marked off three-meter-square areas with string for a study of vegetation, and the elephants came through and were jumping aside, like, “Whoa! That string wasn’t there yesterday.”\u003c/p>\n\u003cp>We don’t think of animals being that aware, but why would we think that way? They’re the ones that are out there living in the wild where it’s dangerous, they’d better be paying close attention. But we picture them as if they’re drifting along in a dream world.\u003c/p>\n\u003cp>The chimpanzees of course were fabulous both at Jane Goodall’s site and in the laboratory. But looking at a chimpanzee like Keo and all that he’d been through as a zoo animal, who was trained to take part in tea parties with children and then made to stand behind bars and have people just stare at him–that has to be hard for any animal. At least he has a better life now. I look at those animals who were brought from somewhere in West Africa and end up at a little dungeon room in Japan sitting under a bare light bulb, and wonder about the animal that does this to other animals.\u003c/p>\n\u003cp>It’s funny that we would question the fact that beings with all the neural anatomy that they have wouldn’t be using it in some way beyond simply a stimulus and response, that they wouldn’t have some way to alter their behaviors. And you think about all the challenges they’re faced with in life and not all of them happen in a repetitious manner as it does in a lab setting. If you could only manage repetition, it doesn’t seem to me that you’d last very long on this planet.\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> What do you hope people get from your book?\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003cstrong>Morell: \u003c/strong>I hope my readers would step back and realize that the birds they listen to, it’s not just an automatic program, but there’s some thinking that’s involved in what they’re doing and their choices in life and to celebrate that. I hope that people stand back and marvel, because it’s a marvelous thing that we’re living on this planet that’s made up of many, many different kinds of beings that all have some kind of mental processes going on, thinking, feeling, experiencing the world. That’s got to be one of the most wonderful things about our planet, that it’s filled with sentient beings. I’m an evolutionary biologist at heart, and I think it’s a marvel that through the processes of natural selection we have a planet of thinking beings. \u003c/p>\n\n",
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"excerpt": "In her new book Animal Wise, Virginia Morell challenges us to recognize the evolutionary roots of animal cognition and to see their rich intellectual and emotional capacities as shaped by natural selection. ",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_2716\" class=\"wp-caption alignnone\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/chimp.jpg\" rel=\"attachment wp-att-2716\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/chimp.jpg\" alt=\"Young male chimp (Credit: Frans de Waal/Emory University)\" width=\"640\" height=\"360\" class=\"size-full wp-image-2716\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Young male chimp (Credit: Frans de Waal/Emory University)\u003c/figcaption>\u003c/figure>\n\u003cp>When I was little, I often consulted our family cat, Scoots, about how we might spend the day. I don’t remember when I realized my parents were teasing me when they asked what he thought of my suggestions, but I do remember wishing there was a way for them to join our conversations. Of course, I didn’t realize it at the time, the mid-1960s, but my parents’ view of animal minds, or the lack thereof, sat squarely within that of mainstream science—which remained stubbornly stagnant on this point for decades. \u003c/p>\n\u003cp>Science’s slow recognition of the rich inner lives of animals is a subject that has long fascinated \u003ca href=\"http://www.gillianmackenzieagency.com/books/authors/48\">Virginia Morell\u003c/a>, a frequent contributor to \u003cem>National Geographic\u003c/em> and \u003cem>Science\u003c/em> and author of the new book \u003ca href=\"http://gillianmackenzieagency.com/books/48\">Animal Wise\u003c/a>. One of the stories that laid the conceptual foundation for her book, \u003ca href=\"http://ngm.nationalgeographic.com/2008/03/animal-minds/virginia-morell-text\">“Minds of Their Own,”\u003c/a> was largely responsible for an all-time best-selling issue for \u003cem>National Geographic\u003c/em>. Morell thinks it resonated with readers, who finally got a chance to see that scientists—not just crazy animal lovers—believe that animals think. \u003c/p>\n\u003cp>Morell will read from Animal Wise at \u003ca href=\"http://bookpassage.com/event/virginia-morell-animal-wise\">Book Passage\u003c/a> in Corte Madera, May 15 at 7 p.m. I spoke with her last month.\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> What inspired you to write this book?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> It was a logical spinoff after doing the \u003ca href=\"https://www.kirkusreviews.com/book-reviews/virginia-morell/ancestral-passions/\">book about the Leakeys\u003c/a>, which explored our fossil ancestry. Then, after seeing chimpanzees in the wild, there were just so many clearcut moments you saw our shared ancestry. My husband and I would come back to the visitors’ guest house where we were staying and describe what we’d seen and we’d talk about people, and then we’d say, I mean chimpanzees. And that fascinated me. Then having my own dog made me interested in these issues. So I began to write about the discoveries that scientists were making about what animals do, both in the wild and in the lab, and you could feel the chipping away of the old standard that everything was a response to a stimulus.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>",
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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>And it puzzled me because, it’s having that evolutionary perspective that makes you wonder, well, if everything’s a response to a stimulus in human animals, what’s changed, how did this dramatic change come about. Why are we unique, why are we special? The focus originally even among people who wanted to understand that cognitive shift was solely on what chimpanzees or other great apes were like, sometimes maybe monkeys, but always on the primate mind. And then as discoveries began to come out of other fields and other animals that people were looking at, you could see that there were more similarities out there than there were differences. \u003c/p>\n\u003cp>I began to wonder what the scientists themselves felt about their discoveries and I wanted to show how we know these things. How do you get around the problem of not being able to ask an animal. When journalists report on the latest science news, we rarely talk about who the animals are and who the researchers are, what drew them to studying their animals. I was quite interested in that too. I always wondered who are the rats who are pressing the levers. Who are these pigeons? What draws a person to [study] that? Surely it’s more than wanting to see the animals as stimulus-response machines.\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> Some of the scientists in your book are pushing the boundaries of what we know about animal cognition. How did you deal with ideas that other scientists might consider “fringe”?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> In the case of \u003ca href=\"http://bio.psu.edu/directory/vab12\">Victoria Braithwaite\u003c/a> (whose studies suggest fish feel pain), there have been challenges to her studies, that’s true. But the question for me was how would I deal with it? Would I do a he said/she said kind of a book, which can be very boring and insider baseball. Or was I going to let these scientists present their side of things and add this to the public debate? And that’s what I chose to do. Certainly her team’s studies were published in high-profile journals, and I was also struck by the comparative study she did, where she showed the fish that were injected with the bee venom versus those that had the saline injection, and the fish with the bee venom changed their behavior. Those fish were adversely affected whereas those with the saline injections were not. To me, that spoke volumes.\u003c/p>\n\u003cfigure id=\"attachment_2713\" class=\"wp-caption alignleft\" style=\"max-width: 240px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/rsz_virginia_morell_credit_michael_mcrae_high_res.jpg\" rel=\"attachment wp-att-2713\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2013/05/rsz_virginia_morell_credit_michael_mcrae_high_res.jpg\" alt=\"Virginia Morell and her dog, Buckaroo\" width=\"240\" height=\"312\" class=\"size-full wp-image-2713\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Virginia Morell and her dog, Buckaroo\u003c/figcaption>\u003c/figure>\n\u003cp>In \u003ca href=\"http://www.brandeis.edu/facultyguide/person.html?emplid=2d3923e829d95e3849ac8001f5c5fa254b5cf400\">Irene Pepperberg’s\u003c/a> case I think she was hamstrung from the beginning. A lot of the questions she was faced with at the beginning we know now were not valid questions because birds have all the key parts of their brain for doing the type of cognitive tasks that Alex [\u003ca href=\"http://www.youtube.com/watch?v=vXoTaZotdHg\">the famed African gray parrot\u003c/a>] was capable of doing. When she first started, it was thought that they lacked some key neural anatomy. Now we know Alex had the mental equipment, the basic biology needed to do the sort of abstract thinking he was doing and that he’s a lifelong vocal learner as we are. \u003c/p>\n\u003cp>I was also struck by the fact that most of the younger scientists, such as \u003ca href=\"http://www.nbb.cornell.edu/berg.shtml\">Karl Berg\u003c/a> and other bird researchers that I’ve spoken to, very much respect Irene’s work. It’s a generational change. I was hesitant when I first started the [National] Geographic story when people asked if I was going to go see Koko and Alex, and I thought, “I don’t know. Those are kind of tainted studies.” And then\u003ca href=\"http://www.zoo.ox.ac.uk/people/view/kacelnik_a.htm\"> Alex Kacelnik\u003c/a> said, “My God, you’ve got to. This is the only animal in the world that’s going to open its mouth and speak to you. And in English!”\u003c/p>\n\u003cp>\u003cstrong>Gross:\u003c/strong> Were there any behaviors or discoveries the scientists told you about that really surprised you?\u003c/p>\n\u003cp>\u003cstrong>Morell:\u003c/strong> I think with every single animal I had that experience. Take the ants. When you saw the size of them, any ant is minuscule but with these, you had to have a magnifying glass to see them, and they were making these amazing decisions. They can go into a crack, they can measure the size of a space and know how large a space they want and how high the ceiling needs to be, how many entrances. They have all these different ways to judge the different requirements they have for just the size of their homes, let alone all the other things they do in their lives. That astonished me. \u003c/p>\n\u003cp>And the fish being able to watch and copy another’s behavior, almost immediately. That requires the fish, the \u003ca href=\"http://www.youtube.com/watch?v=fhBZ40jIo4Q\">archerfish\u003c/a>, to put themselves in the position of the other fish that’s shooting, to make that shot themselves. \u003c/p>\n\u003cp>And Alex was a puzzle. I try and think how on earth a bird would spend its life for Irene, practicing. And the attention to detail that the elephants have, these big animals the size of ships moving across the landscape, they’re paying attention to everything. \u003ca href=\"http://www.wildforlifefoundation.org/joycepoole.html\">Joyce Poole\u003c/a> told me one time she marked off three-meter-square areas with string for a study of vegetation, and the elephants came through and were jumping aside, like, “Whoa! That string wasn’t there yesterday.”\u003c/p>\n\u003cp>We don’t think of animals being that aware, but why would we think that way? They’re the ones that are out there living in the wild where it’s dangerous, they’d better be paying close attention. But we picture them as if they’re drifting along in a dream world.\u003c/p>\n\u003cp>The chimpanzees of course were fabulous both at Jane Goodall’s site and in the laboratory. But looking at a chimpanzee like Keo and all that he’d been through as a zoo animal, who was trained to take part in tea parties with children and then made to stand behind bars and have people just stare at him–that has to be hard for any animal. At least he has a better life now. I look at those animals who were brought from somewhere in West Africa and end up at a little dungeon room in Japan sitting under a bare light bulb, and wonder about the animal that does this to other animals.\u003c/p>\n\u003cp>It’s funny that we would question the fact that beings with all the neural anatomy that they have wouldn’t be using it in some way beyond simply a stimulus and response, that they wouldn’t have some way to alter their behaviors. And you think about all the challenges they’re faced with in life and not all of them happen in a repetitious manner as it does in a lab setting. 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"content": "\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>Morell: \u003c/strong>I hope my readers would step back and realize that the birds they listen to, it’s not just an automatic program, but there’s some thinking that’s involved in what they’re doing and their choices in life and to celebrate that. I hope that people stand back and marvel, because it’s a marvelous thing that we’re living on this planet that’s made up of many, many different kinds of beings that all have some kind of mental processes going on, thinking, feeling, experiencing the world. That’s got to be one of the most wonderful things about our planet, that it’s filled with sentient beings. I’m an evolutionary biologist at heart, and I think it’s a marvel that through the processes of natural selection we have a planet of thinking beings. \u003c/p>\n\n\u003c/div>\u003c/p>",
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"title": "Teen's Science Fair Project: New Diabetes Treatment?",
"headTitle": "Teen's Science Fair Project: New Diabetes Treatment? | KQED",
"content": "\u003cdiv>\n\tSeven Bay Area students are in Phoenix this week for the world’s largest high school science competition.\u003c/div>\n\u003cdiv>\n\t \u003c/div>\n\u003cdiv>\n\tOne sophomore from Walnut Creek was inspired by his grandfather’s Type 1 diabetes. \u003c/div>\n\u003cdiv>\n\t \u003c/div>\n\u003cdiv>\n\tSixteen-year-old Rohan Savoor said he has always been interested in science, but this is the first time he’s been \u003ca href=\"http://www.kqed.org/news/story/2013/05/13/120681/teens_science_fair_project_new_diabetes_treatment?category=science\" target=\"_blank\" rel=\"noopener\">…\u003c/a> \n\u003cp>Source: \u003ca href=\"http://www.kqed.org/news/story/2013/05/13/120681/teens_science_fair_project_new_diabetes_treatment?category=science\" target=\"_blank\" title=\"Teen's Science Fair Project: New Diabetes Treatment?\" rel=\"noopener\">KQED Radio News – Science\u003c/a>\u003c/p>\n\u003c/div>\u003cp>[ad fullwidth]\u003c/p>\u003cp>\u003c/p>\n",
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"excerpt": "\u003cdiv>\n\tSeven Bay Area students are in Phoenix this week for the world’s largest high school science competition.\u003c/div>\n\u003cdiv>\n\t \u003c/div>\n\u003cdiv>\n\tOne sophomore from Walnut Creek was inspired by his grandfather’s Type 1 diabetes. \u003c/div>\n\u003cdiv>\n\t \u003c/div>\n\u003cdiv>\n\tSixteen-year-old Rohan Savoor said he has always been interested in science, but this is the first time he’s been \u003ca href=\"http://www.kqed.org/news/story/2013/05/13/120681/teens_science_fair_project_new_diabetes_treatment?category=science\" target=\"_blank\" rel=\"noopener\">...\u003c/a>",
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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>\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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"disqusTitle": "The Human Microbiome: A Rogue's Gallery",
"title": "The Human Microbiome: A Rogue's Gallery",
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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",
"title": "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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"info": "KQED’s new podcast, Bay Curious, gets to the bottom of the mysteries — both profound and peculiar — that give the Bay Area its unique identity. And we’ll do it with your help! You ask the questions. You decide what Bay Curious investigates. And you join us on the journey to find the answers.",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Bay-Curious-Podcast-Tile-703x703-1.jpg",
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"officialWebsiteLink": "/news/series/baycurious",
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"source": "kqed",
"order": 3
},
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}
},
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"id": "bbc-world-service",
"title": "BBC World Service",
"info": "The day's top stories from BBC News compiled twice daily in the week, once at weekends.",
"airtime": "MON-FRI 9pm-10pm, TUE-FRI 1am-2am",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/BBC-World-Service-Podcast-Tile-360x360-1.jpg",
"officialWebsiteLink": "https://www.bbc.co.uk/sounds/play/live:bbc_world_service",
"meta": {
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"source": "BBC World Service"
},
"link": "/radio/program/bbc-world-service",
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"rss": "https://podcasts.files.bbci.co.uk/p02nq0gn.rss"
}
},
"californiareport": {
"id": "californiareport",
"title": "The California Report",
"tagline": "California, day by day",
"info": "KQED’s statewide radio news program providing daily coverage of issues, trends and public policy decisions.",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/The-California-Report-Podcast-Tile-703x703-1.jpg",
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"officialWebsiteLink": "/californiareport",
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"source": "kqed",
"order": 8
},
"link": "/californiareport",
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}
},
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"title": "The California Report Magazine",
"tagline": "Your state, your stories",
"info": "Every week, The California Report Magazine takes you on a road trip for the ears: to visit the places and meet the people who make California unique. The in-depth storytelling podcast from the California Report.",
"airtime": "FRI 4:30pm-5pm, 6:30pm-7pm, 11pm-11:30pm",
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"officialWebsiteLink": "/californiareportmagazine",
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"order": 10
},
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"google": "https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkM3NjkwNjk1OTAz",
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},
"city-arts": {
"id": "city-arts",
"title": "City Arts & Lectures",
"info": "A one-hour radio program to hear celebrated writers, artists and thinkers address contemporary ideas and values, often discussing the creative process. Please note: tapes or transcripts are not available",
"imageSrc": "https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/05/cityartsandlecture-300x300.jpg",
"officialWebsiteLink": "https://www.cityarts.net/",
"airtime": "SUN 1pm-2pm, TUE 10pm, WED 1am",
"meta": {
"site": "news",
"source": "City Arts & Lectures"
},
"link": "https://www.cityarts.net",
"subscribe": {
"tuneIn": "https://tunein.com/radio/City-Arts-and-Lectures-p692/",
"rss": "https://www.cityarts.net/feed/"
}
},
"closealltabs": {
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"info": "Close All Tabs breaks down how digital culture shapes our world through thoughtful insights and irreverent humor.",
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"officialWebsiteLink": "/podcasts/closealltabs",
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"source": "kqed",
"order": 1
},
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"id": "code-switch-life-kit",
"title": "Code Switch / Life Kit",
"info": "\u003cem>Code Switch\u003c/em>, which listeners will hear in the first part of the hour, has fearless and much-needed conversations about race. Hosted by journalists of color, the show tackles the subject of race head-on, exploring how it impacts every part of society — from politics and pop culture to history, sports and more.\u003cbr />\u003cbr />\u003cem>Life Kit\u003c/em>, which will be in the second part of the hour, guides you through spaces and feelings no one prepares you for — from finances to mental health, from workplace microaggressions to imposter syndrome, from relationships to parenting. The show features experts with real world experience and shares their knowledge. Because everyone needs a little help being human.\u003cbr />\u003cbr />\u003ca href=\"https://www.npr.org/podcasts/510312/codeswitch\">\u003cem>Code Switch\u003c/em> offical site and podcast\u003c/a>\u003cbr />\u003ca href=\"https://www.npr.org/lifekit\">\u003cem>Life Kit\u003c/em> offical site and podcast\u003c/a>\u003cbr />",
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"meta": {
"site": "radio",
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},
"link": "/radio/program/code-switch-life-kit",
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},
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"id": "commonwealth-club",
"title": "Commonwealth Club of California Podcast",
"info": "The Commonwealth Club of California is the nation's oldest and largest public affairs forum. As a non-partisan forum, The Club brings to the public airwaves diverse viewpoints on important topics. The Club's weekly radio broadcast - the oldest in the U.S., dating back to 1924 - is carried across the nation on public radio stations and is now podcasting. Our website archive features audio of our recent programs, as well as selected speeches from our long and distinguished history. This podcast feed is usually updated twice a week and is always un-edited.",
"airtime": "THU 10pm, FRI 1am",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Commonwealth-Club-Podcast-Tile-360x360-1.jpg",
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"meta": {
"site": "news",
"source": "Commonwealth Club of California"
},
"link": "/radio/program/commonwealth-club",
"subscribe": {
"apple": "https://itunes.apple.com/us/podcast/commonwealth-club-of-california-podcast/id976334034?mt=2",
"google": "https://podcasts.google.com/feed/aHR0cDovL3d3dy5jb21tb253ZWFsdGhjbHViLm9yZy9hdWRpby9wb2RjYXN0L3dlZWtseS54bWw",
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},
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"id": "forum",
"title": "Forum",
"tagline": "The conversation starts here",
"info": "KQED’s live call-in program discussing local, state, national and international issues, as well as in-depth interviews.",
"airtime": "MON-FRI 9am-11am, 10pm-11pm",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Forum-Podcast-Tile-703x703-1.jpg",
"imageAlt": "KQED Forum with Mina Kim and Alexis Madrigal",
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"meta": {
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"source": "kqed",
"order": 9
},
"link": "/forum",
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"google": "https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkM5NTU3MzgxNjMz",
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"freakonomics-radio": {
"id": "freakonomics-radio",
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"imageSrc": "https://ww2.kqed.org/news/wp-content/uploads/sites/10/2018/05/freakonomicsRadio.png",
"officialWebsiteLink": "http://freakonomics.com/",
"airtime": "SUN 1am-2am, SAT 3pm-4pm",
"meta": {
"site": "radio",
"source": "WNYC"
},
"link": "/radio/program/freakonomics-radio",
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"apple": "https://itunes.apple.com/us/podcast/freakonomics-radio/id354668519",
"tuneIn": "https://tunein.com/podcasts/WNYC-Podcasts/Freakonomics-Radio-p272293/",
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},
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"id": "fresh-air",
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"link": "/radio/program/fresh-air",
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"apple": "https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=214089682&at=11l79Y&ct=nprdirectory",
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"info": "A live production of NPR and WBUR Boston, in collaboration with stations across the country, Here & Now reflects the fluid world of news as it's happening in the middle of the day, with timely, in-depth news, interviews and conversation. Hosted by Robin Young, Jeremy Hobson and Tonya Mosley.",
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},
"hidden-brain": {
"id": "hidden-brain",
"title": "Hidden Brain",
"info": "Shankar Vedantam uses science and storytelling to reveal the unconscious patterns that drive human behavior, shape our choices and direct our relationships.",
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"airtime": "SUN 7pm-8pm",
"meta": {
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"source": "NPR"
},
"link": "/radio/program/hidden-brain",
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},
"how-i-built-this": {
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"title": "How I Built This with Guy Raz",
"info": "Guy Raz dives into the stories behind some of the world's best known companies. How I Built This weaves a narrative journey about innovators, entrepreneurs and idealists—and the movements they built.",
"imageSrc": "https://ww2.kqed.org/news/wp-content/uploads/sites/10/2018/05/howIBuiltThis.png",
"officialWebsiteLink": "https://www.npr.org/podcasts/510313/how-i-built-this",
"airtime": "SUN 7:30pm-8pm",
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"source": "npr"
},
"link": "/radio/program/how-i-built-this",
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"apple": "https://itunes.apple.com/us/podcast/how-i-built-this-with-guy-raz/id1150510297?mt=2",
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},
"hyphenacion": {
"id": "hyphenacion",
"title": "Hyphenación",
"tagline": "Where conversation and cultura meet",
"info": "What kind of no sabo word is Hyphenación? For us, it’s about living within a hyphenation. Like being a third-gen Mexican-American from the Texas border now living that Bay Area Chicano life. Like Xorje! Each week we bring together a couple of hyphenated Latinos to talk all about personal life choices: family, careers, relationships, belonging … everything is on the table. ",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2025/03/Hyphenacion_FinalAssets_PodcastTile.png",
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"officialWebsiteLink": "/podcasts/hyphenacion",
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"order": 15
},
"link": "/podcasts/hyphenacion",
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},
"jerrybrown": {
"id": "jerrybrown",
"title": "The Political Mind of Jerry Brown",
"tagline": "Lessons from a lifetime in politics",
"info": "The Political Mind of Jerry Brown brings listeners the wisdom of the former Governor, Mayor, and presidential candidate. Scott Shafer interviewed Brown for more than 40 hours, covering the former governor's life and half-century in the political game – and Brown has some lessons he'd like to share. ",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/The-Political-Mind-of-Jerry-Brown-Podcast-Tile-703x703-1.jpg",
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"officialWebsiteLink": "/podcasts/jerrybrown",
"meta": {
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"source": "kqed",
"order": 18
},
"link": "/podcasts/jerrybrown",
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}
},
"latino-usa": {
"id": "latino-usa",
"title": "Latino USA",
"airtime": "MON 1am-2am, SUN 6pm-7pm",
"info": "Latino USA, the radio journal of news and culture, is the only national, English-language radio program produced from a Latino perspective.",
"imageSrc": "https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/04/latinoUsa.jpg",
"officialWebsiteLink": "http://latinousa.org/",
"meta": {
"site": "news",
"source": "npr"
},
"link": "/radio/program/latino-usa",
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"apple": "https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=79681317&at=11l79Y&ct=nprdirectory",
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"rss": "https://feeds.npr.org/510016/podcast.xml"
}
},
"marketplace": {
"id": "marketplace",
"title": "Marketplace",
"info": "Our flagship program, helmed by Kai Ryssdal, examines what the day in money delivered, through stories, conversations, newsworthy numbers and more. Updated Monday through Friday at about 3:30 p.m. PT.",
"airtime": "MON-FRI 4pm-4:30pm, MON-WED 6:30pm-7pm",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Marketplace-Podcast-Tile-360x360-1.jpg",
"officialWebsiteLink": "https://www.marketplace.org/",
"meta": {
"site": "news",
"source": "American Public Media"
},
"link": "/radio/program/marketplace",
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"rss": "https://feeds.publicradio.org/public_feeds/marketplace-pm/rss/rss"
}
},
"masters-of-scale": {
"id": "masters-of-scale",
"title": "Masters of Scale",
"info": "Masters of Scale is an original podcast in which LinkedIn co-founder and Greylock Partner Reid Hoffman sets out to describe and prove theories that explain how great entrepreneurs take their companies from zero to a gazillion in ingenious fashion.",
"airtime": "Every other Wednesday June 12 through October 16 at 8pm (repeats Thursdays at 2am)",
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"officialWebsiteLink": "https://mastersofscale.com/",
"meta": {
"site": "radio",
"source": "WaitWhat"
},
"link": "/radio/program/masters-of-scale",
"subscribe": {
"apple": "http://mastersofscale.app.link/",
"rss": "https://rss.art19.com/masters-of-scale"
}
},
"mindshift": {
"id": "mindshift",
"title": "MindShift",
"tagline": "A podcast about the future of learning and how we raise our kids",
"info": "The MindShift podcast explores the innovations in education that are shaping how kids learn. Hosts Ki Sung and Katrina Schwartz introduce listeners to educators, researchers, parents and students who are developing effective ways to improve how kids learn. We cover topics like how fed-up administrators are developing surprising tactics to deal with classroom disruptions; how listening to podcasts are helping kids develop reading skills; the consequences of overparenting; and why interdisciplinary learning can engage students on all ends of the traditional achievement spectrum. This podcast is part of the MindShift education site, a division of KQED News. KQED is an NPR/PBS member station based in San Francisco. You can also visit the MindShift website for episodes and supplemental blog posts or tweet us \u003ca href=\"https://twitter.com/MindShiftKQED\">@MindShiftKQED\u003c/a> or visit us at \u003ca href=\"/mindshift\">MindShift.KQED.org\u003c/a>",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Mindshift-Podcast-Tile-703x703-1.jpg",
"imageAlt": "KQED MindShift: How We Will Learn",
"officialWebsiteLink": "/mindshift/",
"meta": {
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"source": "kqed",
"order": 12
},
"link": "/podcasts/mindshift",
"subscribe": {
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"google": "https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkM1NzY0NjAwNDI5",
"npr": "https://www.npr.org/podcasts/464615685/mind-shift-podcast",
"stitcher": "https://www.stitcher.com/podcast/kqed/stories-teachers-share",
"spotify": "https://open.spotify.com/show/0MxSpNYZKNprFLCl7eEtyx"
}
},
"morning-edition": {
"id": "morning-edition",
"title": "Morning Edition",
"info": "\u003cem>Morning Edition\u003c/em> takes listeners around the country and the world with multi-faceted stories and commentaries every weekday. Hosts Steve Inskeep, David Greene and Rachel Martin bring you the latest breaking news and features to prepare you for the day.",
"airtime": "MON-FRI 3am-9am",
"imageSrc": "https://cdn.kqed.org/wp-content/uploads/2024/04/Morning-Edition-Podcast-Tile-360x360-1.jpg",
"officialWebsiteLink": "https://www.npr.org/programs/morning-edition/",
"meta": {
"site": "news",
"source": "npr"
},
"link": "/radio/program/morning-edition"
},
"onourwatch": {
"id": "onourwatch",
"title": "On Our Watch",
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