Government Plans to Expand DNA Collection From Migrant Detainees
What a Blue Speck Found in Ancient Teeth Could Reveal About Female Artists in the Middle Ages
Rapid DNA Analysis Used to Help ID Camp Fire Victims
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Scientists Create the Most Precise 3D Map of the Human Genome Yet
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Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome
DNA 2.0: Adding Two Letters to Life’s Alphabet
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On Twitter @lindseyhoshaw","avatar":"https://secure.gravatar.com/avatar/274b07694c998eaa8f26cfabaa941186?s=600&d=blank&r=g","twitter":"lindseyhoshaw","facebook":"lindsey.hoshaw.9","instagram":null,"linkedin":null,"sites":[{"site":"arts","roles":["author"]},{"site":"news","roles":["subscriber"]},{"site":"futureofyou","roles":["editor"]},{"site":"bayareabites","roles":["contributor"]},{"site":"stateofhealth","roles":["author"]},{"site":"science","roles":["edit_theme_options","subscriber"]},{"site":"quest","roles":["edit_post_subscriptions","edit_usergroups","unfiltered_html","unfiltered_upload","leadcoordinator","editor"]},{"site":"food","roles":["contributor"]}],"headData":{"title":"Lindsey Hoshaw | KQED","description":"KQED Contributor","ogImgSrc":"https://secure.gravatar.com/avatar/274b07694c998eaa8f26cfabaa941186?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/274b07694c998eaa8f26cfabaa941186?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/lindseyhoshaw"},"dr-barry-starr":{"type":"authors","id":"6177","meta":{"index":"authors_1591205172","id":"6177","found":true},"name":"Dr. Barry Starr","firstName":"Dr. Barry","lastName":"Starr","slug":"dr-barry-starr","email":"bstarr@thetech.org","display_author_email":false,"staff_mastheads":[],"title":null,"bio":"Dr. Barry Starr (\u003ca href=\"https://twitter.com/geneticsboy\">@geneticsboy\u003c/a>) is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the \u003ca href=\"http://genetics.stanford.edu/\">Stanford Department of Genetics\u003c/a> and \u003ca href=\"http://www.thetech.org/\">The Tech Museum of Innovation\u003c/a>. Together these two partners created the \u003ca href=\"http://www.thetech.org/exhibits/permanent/index.php?sGalKey=gtwt&galKey=lt\">Genetics: Technology with a Twist\u003c/a> exhibition.\r\n\r\nYou can also see \u003ca href=\"https://ww2.kqed.org/science/author/dr-barry-starr/\">additional posts by Barry at KQED Science\u003c/a>, and read his \u003ca href=\"http://science.kqed.org/quest/author/dr-barry-starr/\">previous contributions\u003c/a> to \u003ca href=\"http://science.kqed.org/quest/\">QUEST\u003c/a>, a project dedicated to exploring the Science of Sustainability.","avatar":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twitter":"geneticsboy","facebook":null,"instagram":null,"linkedin":null,"sites":[{"site":"science","roles":["author"]},{"site":"quest","roles":["subscriber"]}],"headData":{"title":"Dr. Barry Starr | KQED","description":null,"ogImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/dr-barry-starr"},"lesleymcclurg":{"type":"authors","id":"11229","meta":{"index":"authors_1591205172","id":"11229","found":true},"name":"Lesley McClurg","firstName":"Lesley","lastName":"McClurg","slug":"lesleymcclurg","email":"lmcclurg@KQED.org","display_author_email":false,"staff_mastheads":["news","science"],"title":"KQED Health Correspondent","bio":"\u003cspan style=\"font-weight: 400;\">Lesley McClurg is a health correspondent and fill-in host. \u003c/span>\u003cspan style=\"font-weight: 400;\">Her work is regularly rebroadcast on numerous NPR and PBS shows. She has won several regional Emmy awards, a regional and a national Edward R. Murrow award. The Association for Health Journalists awarded Lesley best beat coverage. The Society of Professional Journalists has recognized her reporting several times. The Society of Environmental Journalists spotlighted her ongoing coverage of California's historic drought. \u003c/span>\u003cspan style=\"font-weight: 400;\">Before joining KQED in 2016, she covered food and sustainability for Capital Public Radio, the environment for Colorado Public Radio, and reported for both KUOW and KCTS9 in Seattle. \u003c/span>\u003cspan style=\"font-weight: 400;\">When not hunched over her laptop Lesley enjoys skiing with her toddler, surfing with her husband or scheming their next globetrotting adventure. Before motherhood she relished dancing tango till sunrise. When on deadline she fuels herself almost exclusively on chocolate chips.\u003c/span>\r\n\r\n\u003cspan style=\"font-weight: 400;\"> \u003c/span>","avatar":"https://secure.gravatar.com/avatar/3fb78e873af3312f34d0bc1d60a07c7f?s=600&d=blank&r=g","twitter":"lesleywmcclurg","facebook":null,"instagram":null,"linkedin":null,"sites":[{"site":"arts","roles":["author"]},{"site":"news","roles":["editor"]},{"site":"futureofyou","roles":["editor"]},{"site":"stateofhealth","roles":["author"]},{"site":"science","roles":["editor"]}],"headData":{"title":"Lesley McClurg | KQED","description":"KQED Health Correspondent","ogImgSrc":"https://secure.gravatar.com/avatar/3fb78e873af3312f34d0bc1d60a07c7f?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/3fb78e873af3312f34d0bc1d60a07c7f?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/lesleymcclurg"}},"breakingNewsReducer":{},"campaignFinanceReducer":{},"firebase":{"requesting":{},"requested":{},"timestamps":{},"data":{},"ordered":{},"auth":{"isLoaded":false,"isEmpty":true},"authError":null,"profile":{"isLoaded":false,"isEmpty":true},"listeners":{"byId":{},"allIds":[]},"isInitializing":false,"errors":[]},"navBarReducer":{"navBarId":"news","fullView":true,"showPlayer":false},"navMenuReducer":{"menus":[{"key":"menu1","items":[{"name":"News","link":"/","type":"title"},{"name":"Politics","link":"/politics"},{"name":"Science","link":"/science"},{"name":"Education","link":"/educationnews"},{"name":"Housing","link":"/housing"},{"name":"Immigration","link":"/immigration"},{"name":"Criminal Justice","link":"/criminaljustice"},{"name":"Silicon Valley","link":"/siliconvalley"},{"name":"Forum","link":"/forum"},{"name":"The California Report","link":"/californiareport"}]},{"key":"menu2","items":[{"name":"Arts & Culture","link":"/arts","type":"title"},{"name":"Critics’ Picks","link":"/thedolist"},{"name":"Cultural Commentary","link":"/artscommentary"},{"name":"Food & Drink","link":"/food"},{"name":"Bay Area Hip-Hop","link":"/bayareahiphop"},{"name":"Rebel Girls","link":"/rebelgirls"},{"name":"Arts Video","link":"/artsvideos"}]},{"key":"menu3","items":[{"name":"Podcasts","link":"/podcasts","type":"title"},{"name":"Bay Curious","link":"/podcasts/baycurious"},{"name":"Rightnowish","link":"/podcasts/rightnowish"},{"name":"The Bay","link":"/podcasts/thebay"},{"name":"On Our Watch","link":"/podcasts/onourwatch"},{"name":"Mindshift","link":"/podcasts/mindshift"},{"name":"Consider This","link":"/podcasts/considerthis"},{"name":"Political Breakdown","link":"/podcasts/politicalbreakdown"}]},{"key":"menu4","items":[{"name":"Live Radio","link":"/radio","type":"title"},{"name":"TV","link":"/tv","type":"title"},{"name":"Events","link":"/events","type":"title"},{"name":"For Educators","link":"/education","type":"title"},{"name":"Support KQED","link":"/support","type":"title"},{"name":"About","link":"/about","type":"title"},{"name":"Help Center","link":"https://kqed-helpcenter.kqed.org/s","type":"title"}]}]},"pagesReducer":{},"postsReducer":{"stream_live":{"type":"live","id":"stream_live","audioUrl":"https://streams.kqed.org/kqedradio","title":"Live Stream","excerpt":"Live Stream information currently unavailable.","link":"/radio","featImg":"","label":{"name":"KQED Live","link":"/"}},"stream_kqedNewscast":{"type":"posts","id":"stream_kqedNewscast","audioUrl":"https://www.kqed.org/.stream/anon/radio/RDnews/newscast.mp3?_=1","title":"KQED Newscast","featImg":"","label":{"name":"88.5 FM","link":"/"}},"science_1956546":{"type":"posts","id":"science_1956546","meta":{"index":"posts_1591205157","site":"science","id":"1956546","score":null,"sort":[1581356463000]},"guestAuthors":[],"slug":"government-plans-to-expand-dna-collection-from-migrant-detainees","title":"Government Plans to Expand DNA Collection From Migrant Detainees","publishDate":1581356463,"format":"standard","headTitle":"Government Plans to Expand DNA Collection From Migrant Detainees | KQED","labelTerm":{},"content":"\u003cp>The Trump administration has launched a \u003ca href=\"https://www.federalregister.gov/documents/2019/10/22/2019-22877/dna-sample-collection-from-immigration-detainees\" target=\"_blank\" rel=\"noopener noreferrer\">pilot program\u003c/a> to collect DNA samples from migrants in two locations with plans to expand nationwide. The data is sent to the FBI and entered into a criminal database.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">A \u003ca href=\"https://www.dhs.gov/sites/default/files/publications/privacy-pia-dhs080-detaineedna-january2020.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">memo\u003c/a> from the federal Department of Homeland Security says, “prompt DNA-sample collection could be essential to the detection and solution of crimes [aliens] may have committed or may commit in the United States.” \u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The Trump administration also argues collecting DNA will stop migrant adults from smuggling children across the border and falsely posing as their parents. \u003c/span>\u003c/p>\n\u003cp>Immigrant advocates counter that the program will not reduce criminal activity or help solve crimes because \u003ca href=\"https://www.npr.org/2018/05/02/607652253/studies-say-illegal-immigration-does-not-increase-violent-crime\">multiple studies\u003c/a> show that illegal immigration does not result in more lawlessness.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The U.S. Border Patrol agents are learning how to collect DNA from a training video provided by the FBI. People who refuse to submit samples could face misdemeanor charges. \u003c/span>\u003c/p>\n\u003cp>\u003cstrong>Whose DNA is Collected? \u003c/strong>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Federal agents are collecting cheek swabs from people as young as 14 who are in immigration custody at two U.S. locations: at the Canadian border in and around Detroit, and at the official port of entry in Eagle Pass, Texas.\u003c/span>\u003c/p>\n\u003cp>Legal permanent residents and those planning to enter the country legally will not be required to submit samples.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The pilot program began on Jan. 6 and will continue for 90 days. The government plans to expand the program nationwide. \u003c/span>\u003cspan style=\"font-weight: 400\">At present, more than 40,000 people are in medium or long term detention. About a million people circulate through immigration custody each year. \u003c/span>\u003c/p>\n\u003cp>[pullquote]“It casts Latinos as would-be criminals. The racial profiling of this program is unconscionable.” Charleen Adams, geneticist[/pullquote]\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">People land in detention for a variety of reasons: crossing the border illegally, seeking asylum, work site raids, or overstaying a visa. Most \u003c/span>\u003cspan style=\"font-weight: 400\">detainees have \u003ca href=\"https://trac.syr.edu/immigration/reports/583/\" target=\"_blank\" rel=\"noopener noreferrer\">no criminal record\u003c/a>. However, migrants’ DNA\u003c/span>\u003cspan style=\"font-weight: 400\"> samples are registered and held in perpetuity in the FBI criminal database, the Combined Index Data System (CODIS). Historically, that archive has housed genetic information from people who have been arrested, charged or convicted in relation to serious crimes.\u003c/span>\u003c/p>\n\u003cp>\u003cb>Privacy Concerns\u003c/b>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Civil rights advocates worry the expanded genetic testing compromises the privacy of people in detention and their families. Some scientists fear the information could wrongfully target a vulnerable population and lead to false criminal convictions.\u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Vera Eidelman, a staff lawyer with the American Civil Liberties Union’s Speech, Privacy, and Technology Project, calls the program population surveillance. She said the government could use the genetic information to locate family members or even deny people health insurance because DNA is much more powerful than a fingerprint. \u003c/span>\u003c/p>\n\u003cp>“It does not simply identify me as Vera,” Eidelman said. “It also says Vera is related to x, y and z other people. By the way, she also has the BRCA gene or other propensities for medical conditions. It is not simply about identity.”\u003c/p>\n\u003cp>However, Hank Greely, a bioethicist at Stanford University, worries less than Eidelman about these potential uses. Although it is not explicitly clear what genetic information the government will catalog, experts assume it’s the 20 markers that make up the typical DNA profile in the FBI database. This is not a detailed analysis. It’s much less information than a 23andMe or Ancestry.com test.\u003c/p>\n\u003cp>“If you had a kid at the border and wanted to know whether its father was in the CODIS database,” Greely said in an email, “you would likely get hundreds of hits, whether or not the father actually was in the database. That’s not very helpful.”\u003c/p>\n\u003cp>Greely said the government’s efforts to collect DNA are a waste of money because, in his opinion, it’s unlikely the current administration will allow many of the detainees into the country so the likelihood they’ll commit crimes here is also limited.\u003c/p>\n\u003cp>“If there is no good reason to collect personal data, including DNA data, and it isn’t being done voluntarily, then it’s unethical: some risk for no gain is not ethical,” he said.\u003c/p>\n\u003cp>\u003cstrong>\u003cspan style=\"font-weight: 400\">This is not the first time DNA collection efforts have alarmed civil rights advocates. California and other states already collect samples from anyone \u003cem>arrested\u003c/em> for a felony offense. That has helped to solve crimes, but the practice is also \u003ca href=\"https://www.governing.com/topics/public-justice-safety/tns-california-dna-supreme-court.html\" target=\"_blank\" rel=\"noopener noreferrer\">controversial\u003c/a>. \u003c/span>\u003c/strong>\u003c/p>\n\u003cp>\u003cb>Possible Wrongful Convictions\u003c/b>\u003c/p>\n\u003cp>Some scientists fear the program could put the wrong people behind bars because DNA is not foolproof. Someone’s DNA could end up at a crime scene they’ve never visited.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“We pick it [DNA] up and we do transfer it,” said Greg Hampikian, a forensic geneticist at Boise State University. “It’s in the hair we leave behind. It’s on our clothing, cups and utensils.”\u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">DNA can pass between people at a public laundromat, on a toilet seat or even in a bag of donated clothes, and it can last for decades. \u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“DNA is really excellent at identifying people,” Hampikian said. “It is really poor at telling us how it got there.”\u003c/span>\u003c/p>\n\u003cp>The infamous Amanda Knox trial is an example of how DNA can snare innocent people. In 2007 in Perugia, Italy the 20-year-old American college student was accused of stabbing her UK housemate to death. Some of Knox’s DNA was found on the handle of a kitchen knife. A speck of the victim’s DNA was on the blade. Knox spent four years in prison before an appeals court released her, only to be found guilty again. Finally in 2015, after Italian DNA experts reviewed the case Knox was pronounced not guilty.\u003c/p>\n\u003cp>Most Americans find DNA evidence strongly persuasive. A 2015 \u003ca href=\"https://news.gallup.com/poll/1603/crime.aspx\" target=\"_blank\" rel=\"noopener noreferrer\">Gallup poll\u003c/a> showed that 85 percent of Americans consider DNA evidence to be very or completely convincing. Once a DNA sample is entered into a trial as evidence it is very difficult to convince a jury the accused is innocent.\u003c/p>\n\u003cp>\u003cb>Future Implications\u003c/b>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Charleen Adams, a geneticist at City of Hope National Medical Center in Duarte, Calif., \u003c/span>worries the program sets people up to distrust researchers. She\u003cspan style=\"font-weight: 400\"> \u003c/span>noted that people who are forced to relinquish their genetic information at the border may later refuse to volunteer for studies that could directly benefit them, like research on breast cancer in Latinas.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“I feel appalled that that this would slip through without discussion because it is dangerous,” Adams said. “It casts Latinos as would-be criminals. The racial profiling of this program is unconscionable.”\u003c/span>\u003c/p>\n\u003cp>Cybersecurity, she added, is never guaranteed. If the data were to be hacked, they could be used to deny a person employment. Adams also worries about sampling errors at the border, or lab mix-ups that could lead to false negatives or false positives.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n","blocks":[],"excerpt":"Expanded genetic-testing raises concerns about privacy and potential wrongful convictions.","status":"publish","parent":0,"modified":1704847791,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":33,"wordCount":1162},"headData":{"title":"Government Plans to Expand DNA Collection From Migrant Detainees | KQED","description":"Expanded genetic-testing raises concerns about privacy and potential wrongful convictions.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"source":"Genetic Testing","audioUrl":"https://www.kqed.org/.stream/anon/radio/RDnews/2020/02/McCLurgDNABorder.mp3","sticky":false,"path":"/science/1956546/government-plans-to-expand-dna-collection-from-migrant-detainees","audioDuration":247000,"audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>The Trump administration has launched a \u003ca href=\"https://www.federalregister.gov/documents/2019/10/22/2019-22877/dna-sample-collection-from-immigration-detainees\" target=\"_blank\" rel=\"noopener noreferrer\">pilot program\u003c/a> to collect DNA samples from migrants in two locations with plans to expand nationwide. The data is sent to the FBI and entered into a criminal database.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">A \u003ca href=\"https://www.dhs.gov/sites/default/files/publications/privacy-pia-dhs080-detaineedna-january2020.pdf\" target=\"_blank\" rel=\"noopener noreferrer\">memo\u003c/a> from the federal Department of Homeland Security says, “prompt DNA-sample collection could be essential to the detection and solution of crimes [aliens] may have committed or may commit in the United States.” \u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The Trump administration also argues collecting DNA will stop migrant adults from smuggling children across the border and falsely posing as their parents. \u003c/span>\u003c/p>\n\u003cp>Immigrant advocates counter that the program will not reduce criminal activity or help solve crimes because \u003ca href=\"https://www.npr.org/2018/05/02/607652253/studies-say-illegal-immigration-does-not-increase-violent-crime\">multiple studies\u003c/a> show that illegal immigration does not result in more lawlessness.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The U.S. Border Patrol agents are learning how to collect DNA from a training video provided by the FBI. People who refuse to submit samples could face misdemeanor charges. \u003c/span>\u003c/p>\n\u003cp>\u003cstrong>Whose DNA is Collected? \u003c/strong>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Federal agents are collecting cheek swabs from people as young as 14 who are in immigration custody at two U.S. locations: at the Canadian border in and around Detroit, and at the official port of entry in Eagle Pass, Texas.\u003c/span>\u003c/p>\n\u003cp>Legal permanent residents and those planning to enter the country legally will not be required to submit samples.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">The pilot program began on Jan. 6 and will continue for 90 days. The government plans to expand the program nationwide. \u003c/span>\u003cspan style=\"font-weight: 400\">At present, more than 40,000 people are in medium or long term detention. About a million people circulate through immigration custody each year. \u003c/span>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"“It casts Latinos as would-be criminals. The racial profiling of this program is unconscionable.” Charleen Adams, geneticist","name":"pullquote","attributes":{"named":{"label":""},"numeric":[]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">People land in detention for a variety of reasons: crossing the border illegally, seeking asylum, work site raids, or overstaying a visa. Most \u003c/span>\u003cspan style=\"font-weight: 400\">detainees have \u003ca href=\"https://trac.syr.edu/immigration/reports/583/\" target=\"_blank\" rel=\"noopener noreferrer\">no criminal record\u003c/a>. However, migrants’ DNA\u003c/span>\u003cspan style=\"font-weight: 400\"> samples are registered and held in perpetuity in the FBI criminal database, the Combined Index Data System (CODIS). Historically, that archive has housed genetic information from people who have been arrested, charged or convicted in relation to serious crimes.\u003c/span>\u003c/p>\n\u003cp>\u003cb>Privacy Concerns\u003c/b>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Civil rights advocates worry the expanded genetic testing compromises the privacy of people in detention and their families. Some scientists fear the information could wrongfully target a vulnerable population and lead to false criminal convictions.\u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Vera Eidelman, a staff lawyer with the American Civil Liberties Union’s Speech, Privacy, and Technology Project, calls the program population surveillance. She said the government could use the genetic information to locate family members or even deny people health insurance because DNA is much more powerful than a fingerprint. \u003c/span>\u003c/p>\n\u003cp>“It does not simply identify me as Vera,” Eidelman said. “It also says Vera is related to x, y and z other people. By the way, she also has the BRCA gene or other propensities for medical conditions. It is not simply about identity.”\u003c/p>\n\u003cp>However, Hank Greely, a bioethicist at Stanford University, worries less than Eidelman about these potential uses. Although it is not explicitly clear what genetic information the government will catalog, experts assume it’s the 20 markers that make up the typical DNA profile in the FBI database. This is not a detailed analysis. It’s much less information than a 23andMe or Ancestry.com test.\u003c/p>\n\u003cp>“If you had a kid at the border and wanted to know whether its father was in the CODIS database,” Greely said in an email, “you would likely get hundreds of hits, whether or not the father actually was in the database. That’s not very helpful.”\u003c/p>\n\u003cp>Greely said the government’s efforts to collect DNA are a waste of money because, in his opinion, it’s unlikely the current administration will allow many of the detainees into the country so the likelihood they’ll commit crimes here is also limited.\u003c/p>\n\u003cp>“If there is no good reason to collect personal data, including DNA data, and it isn’t being done voluntarily, then it’s unethical: some risk for no gain is not ethical,” he said.\u003c/p>\n\u003cp>\u003cstrong>\u003cspan style=\"font-weight: 400\">This is not the first time DNA collection efforts have alarmed civil rights advocates. California and other states already collect samples from anyone \u003cem>arrested\u003c/em> for a felony offense. That has helped to solve crimes, but the practice is also \u003ca href=\"https://www.governing.com/topics/public-justice-safety/tns-california-dna-supreme-court.html\" target=\"_blank\" rel=\"noopener noreferrer\">controversial\u003c/a>. \u003c/span>\u003c/strong>\u003c/p>\n\u003cp>\u003cb>Possible Wrongful Convictions\u003c/b>\u003c/p>\n\u003cp>Some scientists fear the program could put the wrong people behind bars because DNA is not foolproof. Someone’s DNA could end up at a crime scene they’ve never visited.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“We pick it [DNA] up and we do transfer it,” said Greg Hampikian, a forensic geneticist at Boise State University. “It’s in the hair we leave behind. It’s on our clothing, cups and utensils.”\u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">DNA can pass between people at a public laundromat, on a toilet seat or even in a bag of donated clothes, and it can last for decades. \u003c/span>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“DNA is really excellent at identifying people,” Hampikian said. “It is really poor at telling us how it got there.”\u003c/span>\u003c/p>\n\u003cp>The infamous Amanda Knox trial is an example of how DNA can snare innocent people. In 2007 in Perugia, Italy the 20-year-old American college student was accused of stabbing her UK housemate to death. Some of Knox’s DNA was found on the handle of a kitchen knife. A speck of the victim’s DNA was on the blade. Knox spent four years in prison before an appeals court released her, only to be found guilty again. Finally in 2015, after Italian DNA experts reviewed the case Knox was pronounced not guilty.\u003c/p>\n\u003cp>Most Americans find DNA evidence strongly persuasive. A 2015 \u003ca href=\"https://news.gallup.com/poll/1603/crime.aspx\" target=\"_blank\" rel=\"noopener noreferrer\">Gallup poll\u003c/a> showed that 85 percent of Americans consider DNA evidence to be very or completely convincing. Once a DNA sample is entered into a trial as evidence it is very difficult to convince a jury the accused is innocent.\u003c/p>\n\u003cp>\u003cb>Future Implications\u003c/b>\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">Charleen Adams, a geneticist at City of Hope National Medical Center in Duarte, Calif., \u003c/span>worries the program sets people up to distrust researchers. She\u003cspan style=\"font-weight: 400\"> \u003c/span>noted that people who are forced to relinquish their genetic information at the border may later refuse to volunteer for studies that could directly benefit them, like research on breast cancer in Latinas.\u003c/p>\n\u003cp>\u003cspan style=\"font-weight: 400\">“I feel appalled that that this would slip through without discussion because it is dangerous,” Adams said. “It casts Latinos as would-be criminals. The racial profiling of this program is unconscionable.”\u003c/span>\u003c/p>\n\u003cp>Cybersecurity, she added, is never guaranteed. If the data were to be hacked, they could be used to deny a person employment. Adams also worries about sampling errors at the border, or lab mix-ups that could lead to false negatives or false positives.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/1956546/government-plans-to-expand-dna-collection-from-migrant-detainees","authors":["11229"],"categories":["science_39","science_3890","science_40"],"tags":["science_305","science_3370","science_3514"],"featImg":"science_1956727","label":"source_science_1956546"},"science_1936646":{"type":"posts","id":"science_1936646","meta":{"index":"posts_1591205157","site":"science","id":"1936646","score":null,"sort":[1547222410000]},"guestAuthors":[],"slug":"what-a-blue-speck-found-in-ancient-teeth-could-reveal-about-female-artists-in-the-middle-ages","title":"What a Blue Speck Found in Ancient Teeth Could Reveal About Female Artists in the Middle Ages","publishDate":1547222410,"format":"standard","headTitle":"What a Blue Speck Found in Ancient Teeth Could Reveal About Female Artists in the Middle Ages | KQED","labelTerm":{},"content":"\u003cp>Tiny bits of blue pigment found in the teeth of a medieval skeleton reveal that more than 850 years ago, this seemingly ordinary woman was very likely involved in the production of lavishly illustrated sacred texts.\u003c/p>\n\u003cp>The unexpected discovery, \u003ca href=\"http://advances.sciencemag.org/content/5/1/eaau7126\">described\u003c/a> in the journal \u003cem>Science Advances,\u003c/em> astonished scientists who weren’t setting out to study female artists in the Middle Ages. It adds to a growing recognition that women, and not just monks, labored as the anonymous scribes who painstakingly copied manuscripts and decorated the pages to dazzle the eye.\u003c/p>\n\u003cp>This particular woman lived in a small religious community at Dalheim, Germany. Little is known about life there, says \u003ca href=\"http://christinawarinner.com/about-us/christina-warinner/\">Christina Warinner\u003c/a> of the Max Planck Institute for the Science of Human History in Germany.\u003c/p>\n\u003cp>“Basically all that remains are the stone foundations. A broken comb was found, but almost nothing else,” Warinner says. “There are no books that survived. There’s no art that survives. It’s known only from a handful of scraps of text that mention it in passing.”\u003c/p>\n\u003cp>She and a colleague were examining the teeth of skeletons from this community’s cemetery to see what had been preserved in the dental calculus, or tartar. Tartar forms from sticky plaque that traps remnants of food, bacteria and even pollen and then hardens over time.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>“It’s really an extraordinary material,” Warinner says. “It’s actually the only part of your body that fossilizes while you’re still alive.”\u003c/p>\n\u003cfigure id=\"attachment_1936652\" class=\"wp-caption alignright\" style=\"max-width: 800px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-1936652\" src=\"https://ww2.kqed.org/science/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-800x600.jpg\" alt=\"\" width=\"800\" height=\"600\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-800x600.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-160x120.jpg 160w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-768x576.jpg 768w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-240x180.jpg 240w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-375x281.jpg 375w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-520x390.jpg 520w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200.jpg 915w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003cfigcaption class=\"wp-caption-text\">During the European Middle Ages, Afghanistan was the only known source of the rare blue stone lapis lazuli. \u003ccite>(Christina Warinner/Science Advances)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Her colleague \u003ca href=\"https://www.york.ac.uk/archaeology/staff/research-staff/anita-radini/\">Anita Radini\u003c/a>, of the University of York in the United Kingdom, spotted something bright blue in the dental sample from this woman.\u003c/p>\n\u003cp>“It was absolutely unbelievable. It almost looked like there were robins’ eggs on the microscope slide — they were such vibrant blue particles,” Warinner recalls. “I remember joking around at the time that maybe we discovered an artist painting with lapis lazuli.”\u003c/p>\n\u003cp>The idea seemed absurd. After all, lapis lazuli was one of the most expensive pigments known in the Middle Ages. At the time, it came from just one source — a region of Afghanistan — and was used only by artists of exceptional skill.\u003c/p>\n\u003cp>“It was rare,” Warinner says. “It’s really iconic. It’s kind of the blue that we associate with the Middles Ages that’s absent in Roman art.”\u003c/p>\n\u003cp>The researchers turned to technologies that could analyze the elemental composition of the microscopic particles as well as the mineral structure. “And ultimately we did find that it was indeed lapis lazuli, which was really, really surprising,” Warinner says. “Once it all came together that this was lapis lazuli, and this was a woman, and she was in this kind of small, remote place, really far away from where this lapis lazuli would have come from or been traded from, it was pretty extraordinary.”\u003c/p>\n\u003cfigure id=\"attachment_1936647\" class=\"wp-caption alignnone\" style=\"max-width: 639px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-1936647\" src=\"https://ww2.kqed.org/science/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead.jpe\" alt=\"\" width=\"639\" height=\"622\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead.jpe 639w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-160x156.jpe 160w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-240x234.jpe 240w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-375x365.jpe 375w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-520x506.jpe 520w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-32x32.jpe 32w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-50x50.jpe 50w\" sizes=\"(max-width: 639px) 100vw, 639px\">\u003cfigcaption class=\"wp-caption-text\">This image shows Guda, a 12th century nun, and the inscription reads, “Guda, a sinful woman, wrote and painted this book.” It’s a rare example of a manuscript signed by a female scribe. \u003ccite>(Frankfurt University Library)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Warinner reached out to \u003ca href=\"https://history.osu.edu/people/beach.174\">Alison Beach\u003c/a>, a professor of medieval history at Ohio State University in Columbus. “I realized this is a really sensational find,” Beach says.\u003c/p>\n\u003cp>“There’s quite a bit of evidence of female contributions to book production. And it’s gotten more attention in the past 20 years,” Beach says. “But I still think that image of the monk as the producer of books is very central and very resilient.”\u003c/p>\n\u003cp>Of those books that were signed with the name of the scribe before the 12th century, less than 1 percent can be attributed to women, the researchers write in their report. But Beach says it’s just impossible to know how widespread women’s participation was, because many libraries of medieval books have been lost to history. What’s more, most of the surviving books from this period were produced by scribes who did not sign their work.\u003c/p>\n\u003cp>“I’m still trying to convince colleagues that they should immediately consider female book production or ownership or use when they encounter an anonymous manuscript in the Middles Ages,” Beach says. “Was ‘anonymous’ a man or a woman? We really just don’t know for most of them.”\u003c/p>\n\u003cp>The researchers considered various explanations for how the blue pigment ended up in the woman’s teeth. One possibility is that she wasn’t an artist but rather engaged in devotional kissing of a decorated text. “You’d have to be doing a lot of kissing of a book over a lot of time to get that much lapis lazuli pigment,” Beach says. “That one seemed, to me, to be the least plausible.”\u003c/p>\n\u003cp>Another possibility was that the woman consumed the pigment as a kind of medicine. That also seems unlikely, given the lack of evidence that this was common in Germany in the 11th and 12th centuries. What’s more, the lapis lazuli residue was found more toward the front of the mouth than the back.\u003c/p>\n\u003cp>“I thought they made a nice case that because it is up near the lips, that it was most likely related to the notion of moistening the brush,” says \u003ca href=\"https://blair.vanderbilt.edu/bio/cynthia-cyrus\">Cynthia Cyrus\u003c/a> of Vanderbilt University, who has studied medieval scribes associated with women’s convents but was not part of the research team. “As you put the tip of the brush into your mouth to bring it to a point, a little bit of the pigment residue then makes its way into the dental structure. That would explain the differential between back of mouth and front of mouth.”\u003c/p>\n\u003cp>It is true that simply grinding lapis lazuli can produce fine, airborne dust that ends up on the lips and in the saliva, the researchers found — because Radini tried it herself.\u003c/p>\n\u003cp>However, given the small size of this religious community — only around 15 people — it’s likely that this artist produced her own materials rather than making them for sale or for someone else.\u003c/p>\n\u003cp>“You’re going to be creating your own pigments and using your pigments,” Cyrus says. “This individual may, in fact, have been doing both of those activities.”\u003c/p>\n\u003cp>In Cyrus’ view, this finding is extraordinary.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>“It is a brand-new kind of evidence for scribal activity, and one that we haven’t been on the alert for,” she says. “We now know that evidence from teeth, and other skeletal remains, can really point towards what the daily life of a particular monastery was like. That will lead us to ask different questions when we’re doing excavations and combine different kinds of evidence to get a better understanding.”\u003c/p>\n\u003cdiv class=\"fullattribution\">\u003cem>Copyright 2019 NPR. To see more, visit \u003ca href=\"http://www.npr.org\">www.npr.org\u003c/a>.\u003cimg decoding=\"async\" src=\"https://www.google-analytics.com/__utm.gif?utmac=UA-5828686-4&utmdt=A+Blue+Clue+In+Medieval+Teeth+May+Bespeak+A+Woman%27s+Artistry+Circa+A.D.+1000+&utme=8(APIKey)9(MDAxOTAwOTE4MDEyMTkxMDAzNjczZDljZA004)\">\u003c/em>\u003c/div>\n\n","blocks":[],"excerpt":"Analysis of fossilized dental tartar of a medieval woman buried in a German monastery reveals specks of blue to be lapis lazuli — a luxurious pigment used to create gorgeous illuminated manuscripts.","status":"publish","parent":0,"modified":1704927205,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":25,"wordCount":1211},"headData":{"title":"What a Blue Speck Found in Ancient Teeth Could Reveal About Female Artists in the Middle Ages | KQED","description":"Analysis of fossilized dental tartar of a medieval woman buried in a German monastery reveals specks of blue to be lapis lazuli — a luxurious pigment used to create gorgeous illuminated manuscripts.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"source":"Science","sticky":false,"nprByline":"Nell Greenfieldboyce\u003c/br>","nprStoryId":"683283982","nprApiLink":"http://api.npr.org/query?id=683283982&apiKey=MDAxOTAwOTE4MDEyMTkxMDAzNjczZDljZA004","nprHtmlLink":"https://www.npr.org/sections/health-shots/2019/01/09/683283982/a-blue-clue-in-medieval-teeth-may-bespeak-a-womans-artistry-circa-1-000-a-d?ft=nprml&f=683283982","nprRetrievedStory":"1","nprPubDate":"Wed, 09 Jan 2019 19:18:00 -0500","nprStoryDate":"Wed, 09 Jan 2019 14:05:00 -0500","nprLastModifiedDate":"Wed, 09 Jan 2019 19:18:01 -0500","nprAudio":"https://ondemand.npr.org/anon.npr-mp3/npr/atc/2019/01/20190109_atc_a_blue_clue_in_medieval_teeth_may_bespeak_a_womans_artistry_circa_1000_ad.mp3?orgId=1&topicId=1128&d=215&p=2&story=683283982&ft=nprml&f=683283982","nprAudioM3u":"http://api.npr.org/m3u/1683732144-d4015a.m3u?orgId=1&topicId=1128&d=215&p=2&story=683283982&ft=nprml&f=683283982","audioTrackLength":216,"path":"/science/1936646/what-a-blue-speck-found-in-ancient-teeth-could-reveal-about-female-artists-in-the-middle-ages","audioUrl":"https://ondemand.npr.org/anon.npr-mp3/npr/atc/2019/01/20190109_atc_a_blue_clue_in_medieval_teeth_may_bespeak_a_womans_artistry_circa_1000_ad.mp3?orgId=1&topicId=1128&d=215&p=2&story=683283982&ft=nprml&f=683283982","parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>Tiny bits of blue pigment found in the teeth of a medieval skeleton reveal that more than 850 years ago, this seemingly ordinary woman was very likely involved in the production of lavishly illustrated sacred texts.\u003c/p>\n\u003cp>The unexpected discovery, \u003ca href=\"http://advances.sciencemag.org/content/5/1/eaau7126\">described\u003c/a> in the journal \u003cem>Science Advances,\u003c/em> astonished scientists who weren’t setting out to study female artists in the Middle Ages. It adds to a growing recognition that women, and not just monks, labored as the anonymous scribes who painstakingly copied manuscripts and decorated the pages to dazzle the eye.\u003c/p>\n\u003cp>This particular woman lived in a small religious community at Dalheim, Germany. Little is known about life there, says \u003ca href=\"http://christinawarinner.com/about-us/christina-warinner/\">Christina Warinner\u003c/a> of the Max Planck Institute for the Science of Human History in Germany.\u003c/p>\n\u003cp>“Basically all that remains are the stone foundations. A broken comb was found, but almost nothing else,” Warinner says. “There are no books that survived. There’s no art that survives. It’s known only from a handful of scraps of text that mention it in passing.”\u003c/p>\n\u003cp>She and a colleague were examining the teeth of skeletons from this community’s cemetery to see what had been preserved in the dental calculus, or tartar. Tartar forms from sticky plaque that traps remnants of food, bacteria and even pollen and then hardens over time.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“It’s really an extraordinary material,” Warinner says. “It’s actually the only part of your body that fossilizes while you’re still alive.”\u003c/p>\n\u003cfigure id=\"attachment_1936652\" class=\"wp-caption alignright\" style=\"max-width: 800px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-1936652\" src=\"https://ww2.kqed.org/science/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-800x600.jpg\" alt=\"\" width=\"800\" height=\"600\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-800x600.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-160x120.jpg 160w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-768x576.jpg 768w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-240x180.jpg 240w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-375x281.jpg 375w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200-520x390.jpg 520w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/radini4hr-700e6788a93e5ef898448c2569c3ca8519910954-s1200.jpg 915w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003cfigcaption class=\"wp-caption-text\">During the European Middle Ages, Afghanistan was the only known source of the rare blue stone lapis lazuli. \u003ccite>(Christina Warinner/Science Advances)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Her colleague \u003ca href=\"https://www.york.ac.uk/archaeology/staff/research-staff/anita-radini/\">Anita Radini\u003c/a>, of the University of York in the United Kingdom, spotted something bright blue in the dental sample from this woman.\u003c/p>\n\u003cp>“It was absolutely unbelievable. It almost looked like there were robins’ eggs on the microscope slide — they were such vibrant blue particles,” Warinner recalls. “I remember joking around at the time that maybe we discovered an artist painting with lapis lazuli.”\u003c/p>\n\u003cp>The idea seemed absurd. After all, lapis lazuli was one of the most expensive pigments known in the Middle Ages. At the time, it came from just one source — a region of Afghanistan — and was used only by artists of exceptional skill.\u003c/p>\n\u003cp>“It was rare,” Warinner says. “It’s really iconic. It’s kind of the blue that we associate with the Middles Ages that’s absent in Roman art.”\u003c/p>\n\u003cp>The researchers turned to technologies that could analyze the elemental composition of the microscopic particles as well as the mineral structure. “And ultimately we did find that it was indeed lapis lazuli, which was really, really surprising,” Warinner says. “Once it all came together that this was lapis lazuli, and this was a woman, and she was in this kind of small, remote place, really far away from where this lapis lazuli would have come from or been traded from, it was pretty extraordinary.”\u003c/p>\n\u003cfigure id=\"attachment_1936647\" class=\"wp-caption alignnone\" style=\"max-width: 639px\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-1936647\" src=\"https://ww2.kqed.org/science/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead.jpe\" alt=\"\" width=\"639\" height=\"622\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead.jpe 639w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-160x156.jpe 160w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-240x234.jpe 240w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-375x365.jpe 375w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-520x506.jpe 520w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-32x32.jpe 32w, https://cdn.kqed.org/wp-content/uploads/sites/35/2019/01/lapis-1_enl-75cdb0a59fc72b4a25bd476677f69e61c92c3ead-50x50.jpe 50w\" sizes=\"(max-width: 639px) 100vw, 639px\">\u003cfigcaption class=\"wp-caption-text\">This image shows Guda, a 12th century nun, and the inscription reads, “Guda, a sinful woman, wrote and painted this book.” It’s a rare example of a manuscript signed by a female scribe. \u003ccite>(Frankfurt University Library)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>Warinner reached out to \u003ca href=\"https://history.osu.edu/people/beach.174\">Alison Beach\u003c/a>, a professor of medieval history at Ohio State University in Columbus. “I realized this is a really sensational find,” Beach says.\u003c/p>\n\u003cp>“There’s quite a bit of evidence of female contributions to book production. And it’s gotten more attention in the past 20 years,” Beach says. “But I still think that image of the monk as the producer of books is very central and very resilient.”\u003c/p>\n\u003cp>Of those books that were signed with the name of the scribe before the 12th century, less than 1 percent can be attributed to women, the researchers write in their report. But Beach says it’s just impossible to know how widespread women’s participation was, because many libraries of medieval books have been lost to history. What’s more, most of the surviving books from this period were produced by scribes who did not sign their work.\u003c/p>\n\u003cp>“I’m still trying to convince colleagues that they should immediately consider female book production or ownership or use when they encounter an anonymous manuscript in the Middles Ages,” Beach says. “Was ‘anonymous’ a man or a woman? We really just don’t know for most of them.”\u003c/p>\n\u003cp>The researchers considered various explanations for how the blue pigment ended up in the woman’s teeth. One possibility is that she wasn’t an artist but rather engaged in devotional kissing of a decorated text. “You’d have to be doing a lot of kissing of a book over a lot of time to get that much lapis lazuli pigment,” Beach says. “That one seemed, to me, to be the least plausible.”\u003c/p>\n\u003cp>Another possibility was that the woman consumed the pigment as a kind of medicine. That also seems unlikely, given the lack of evidence that this was common in Germany in the 11th and 12th centuries. What’s more, the lapis lazuli residue was found more toward the front of the mouth than the back.\u003c/p>\n\u003cp>“I thought they made a nice case that because it is up near the lips, that it was most likely related to the notion of moistening the brush,” says \u003ca href=\"https://blair.vanderbilt.edu/bio/cynthia-cyrus\">Cynthia Cyrus\u003c/a> of Vanderbilt University, who has studied medieval scribes associated with women’s convents but was not part of the research team. “As you put the tip of the brush into your mouth to bring it to a point, a little bit of the pigment residue then makes its way into the dental structure. That would explain the differential between back of mouth and front of mouth.”\u003c/p>\n\u003cp>It is true that simply grinding lapis lazuli can produce fine, airborne dust that ends up on the lips and in the saliva, the researchers found — because Radini tried it herself.\u003c/p>\n\u003cp>However, given the small size of this religious community — only around 15 people — it’s likely that this artist produced her own materials rather than making them for sale or for someone else.\u003c/p>\n\u003cp>“You’re going to be creating your own pigments and using your pigments,” Cyrus says. “This individual may, in fact, have been doing both of those activities.”\u003c/p>\n\u003cp>In Cyrus’ view, this finding is extraordinary.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“It is a brand-new kind of evidence for scribal activity, and one that we haven’t been on the alert for,” she says. “We now know that evidence from teeth, and other skeletal remains, can really point towards what the daily life of a particular monastery was like. That will lead us to ask different questions when we’re doing excavations and combine different kinds of evidence to get a better understanding.”\u003c/p>\n\u003cdiv class=\"fullattribution\">\u003cem>Copyright 2019 NPR. To see more, visit \u003ca href=\"http://www.npr.org\">www.npr.org\u003c/a>.\u003cimg decoding=\"async\" src=\"https://www.google-analytics.com/__utm.gif?utmac=UA-5828686-4&utmdt=A+Blue+Clue+In+Medieval+Teeth+May+Bespeak+A+Woman%27s+Artistry+Circa+A.D.+1000+&utme=8(APIKey)9(MDAxOTAwOTE4MDEyMTkxMDAzNjczZDljZA004)\">\u003c/em>\u003c/div>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/1936646/what-a-blue-speck-found-in-ancient-teeth-could-reveal-about-female-artists-in-the-middle-ages","authors":["byline_science_1936646"],"categories":["science_35","science_38","science_16","science_40"],"tags":["science_305","science_349","science_218","science_3838"],"featImg":"science_1936649","label":"source_science_1936646"},"science_1934691":{"type":"posts","id":"science_1934691","meta":{"index":"posts_1591205157","site":"science","id":"1934691","score":null,"sort":[1542756768000]},"guestAuthors":[],"slug":"rapid-dna-analysis-used-to-help-id-camp-fire-victims","title":"Rapid DNA Analysis Used to Help ID Camp Fire Victims","publishDate":1542756768,"format":"standard","headTitle":"Rapid DNA Analysis Used to Help ID Camp Fire Victims | KQED","labelTerm":{"site":"science"},"content":"\u003cp>SACRAMENTO, Calif. (AP) — Authorities are using a powerful tool in their effort to identify the scores of people killed by the wildfire that ripped through Northern California: rapid DNA testing that produces results in just two hours.\u003c/p>\n\u003cp>The system can analyze DNA from bone fragments or other remains, then match it to genetic material provided by relatives of the missing. But the technology depends on people coming forward to give a DNA sample via a cheek swab, and so far, there are not nearly as many volunteers as authorities had hoped for.\u003c/p>\n\u003caside class=\"pullquote alignright\">‘This is the one way I could contribute to helping find my uncle.’\u003c/aside>\n\u003cp>As of Tuesday, nearly two weeks after the inferno devastated the town of Paradise and surrounding areas, the number of confirmed dead stood at 79, and the sheriff’s list of those unaccounted for had about 700 names.\u003c/p>\n\u003cp>But only about 60 people had provided samples to pop-up labs at the Butte County Sheriff’s office in Oroville and an old Sears building in Chico, where the Federal Emergency Management Agency set up a disaster relief center, said Annette Mattern, a spokeswoman for ANDE, the Longmont, Colorado, company that is donating the technology.\u003c/p>\n\u003cp>“We need hundreds,” Mattern said. “We need a big enough sample for us to make a positive ID on these and to also give a better idea of how many losses there actually are.”\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Confusion and conflicting information, the inability of relatives to travel to Northern California and mistrust of the government may be contributing to the low number.\u003c/p>\n\u003cp>Tara Quinones hadn’t heard anything from her uncle, David Marbury, for eight days before she drove north from the San Francisco Bay Area to give a sample Friday. A worker used a small tool to scrape her cheek, took three swabs of skin and asked her detailed questions about who she was looking for and their relationship.\u003c/p>\n\u003cp>The uncle’s landlord confirmed his house burned down with his vehicle still in the garage, but Quinones had no idea if any remains were found. Marbury’s name keeps going on and off the ever-changing list of the missing.\u003c/p>\n\u003cp>“I did it just to be proactive,” Quinones said Monday. “This is the one way I could contribute to helping find my uncle.”\u003c/p>\n\u003cp>Some of those who have given DNA came forward, like Quinones, after learning about the identification effort in their desperate search for a loved one, others after the sheriff’s office called to say that remains that probably belonged to a family member had been found.\u003c/p>\n\u003cp>Mattern declined to say Tuesday how many victims ANDE’s technology has helped identify. Sheriff Kory Honea’s office did not immediately respond to requests for comment.\u003c/p>\n\u003cp>The fire was 70 percent contained Tuesday. Rain in the forecast for Wednesday through Thanksgiving weekend could aid in fighting the fire but could also bring flash floods and complicate efforts to recover remains.\u003c/p>\n\u003cp>Once DNA is extracted from the remains, it is placed in a vial that goes into a black machine that looks like a bulky computer printer. It takes just two hours to process the material and get a DNA profile; traditional methods can take days or weeks. If a relative’s DNA is already in the system, a match will pop up right away.\u003c/p>\n\u003cp>Mattern said it has been surprisingly easy to get DNA from remains, despite the devastating damage done by the flames.\u003c/p>\n\u003cp>“We went in with pretty measured expectations, we didn’t know what we were walking into,” she said. “We have a tremendous database now of the victims of the fire.”\u003c/p>\n\u003cp>Ruth Dickover, director of the forensic science graduate program at the University of California-Davis, said that scientists have long been able to extract DNA from bone — a process that involves pulverizing the bone — but things can become more complicated if the remains of multiple people are mixed together.\u003c/p>\n\u003cp>“What’s left may not give you a nice beautiful profile,” she said.\u003cbr>\nANDE won a contract in 2009 to do research and development for federal agencies, and the company’s technology has been used in pilot programs for several years. Over the summer, it won FBI approval for use in accredited labs. Law enforcement agencies in Utah, New York and Miami have used the technology, as has the military.\u003c/p>\n\u003cp>This is the first time ANDE has helped identify victims after a natural disaster. The company has donated seven machines and about a dozen workers to the effort.\u003c/p>\n\u003cp>Sarah Warren drove an hour and a half from Redding on Monday to report her uncle, Devan Ruel, as missing. The sheriff’s office gave her a number to call about missing people, and when she called, she was told authorities would contact her if they needed her DNA, she said.\u003cbr>\nShe said no one told her about the collection desk at the old Sears, so she returned home without providing one.\u003c/p>\n\u003cp>“I could have done that so easily, just to be safe,” she said.\u003c/p>\n\u003cp>Warren hadn’t talked to Ruel in about eight years and said the family did not have an address for him.\u003c/p>\n\u003cp>“He was just an off-the-grid type of guy,” she said. “If he did perish that way it would be horrific. It deeply, deeply saddens me to even consider that being a possibility.”\u003c/p>\n\u003cp>Mattern said the sheriff’s office is looking for a way to make it easier for families who don’t live in Northern California to provide samples.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>And in hopes of easing fears that the DNA will be misused, the sheriff’s office and the company gave assurances it will be deleted once it is no longer needed.\u003c/p>\n\n","blocks":[],"excerpt":"With hundreds still missing, Butte County is searching for the quickest way to identify remains found in the devastating Camp Fire. Authorities hope more DNA volunteers will come forward.","status":"publish","parent":0,"modified":1704927300,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":26,"wordCount":990},"headData":{"title":"Rapid DNA Analysis Used to Help ID Camp Fire Victims | KQED","description":"With hundreds still missing, Butte County is searching for the quickest way to identify remains found in the devastating Camp Fire. Authorities hope more DNA volunteers will come forward.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"nprByline":"Kathleen Ronayne\u003cbr>Associated Press","path":"/science/1934691/rapid-dna-analysis-used-to-help-id-camp-fire-victims","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>SACRAMENTO, Calif. (AP) — Authorities are using a powerful tool in their effort to identify the scores of people killed by the wildfire that ripped through Northern California: rapid DNA testing that produces results in just two hours.\u003c/p>\n\u003cp>The system can analyze DNA from bone fragments or other remains, then match it to genetic material provided by relatives of the missing. But the technology depends on people coming forward to give a DNA sample via a cheek swab, and so far, there are not nearly as many volunteers as authorities had hoped for.\u003c/p>\n\u003caside class=\"pullquote alignright\">‘This is the one way I could contribute to helping find my uncle.’\u003c/aside>\n\u003cp>As of Tuesday, nearly two weeks after the inferno devastated the town of Paradise and surrounding areas, the number of confirmed dead stood at 79, and the sheriff’s list of those unaccounted for had about 700 names.\u003c/p>\n\u003cp>But only about 60 people had provided samples to pop-up labs at the Butte County Sheriff’s office in Oroville and an old Sears building in Chico, where the Federal Emergency Management Agency set up a disaster relief center, said Annette Mattern, a spokeswoman for ANDE, the Longmont, Colorado, company that is donating the technology.\u003c/p>\n\u003cp>“We need hundreds,” Mattern said. “We need a big enough sample for us to make a positive ID on these and to also give a better idea of how many losses there actually are.”\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Confusion and conflicting information, the inability of relatives to travel to Northern California and mistrust of the government may be contributing to the low number.\u003c/p>\n\u003cp>Tara Quinones hadn’t heard anything from her uncle, David Marbury, for eight days before she drove north from the San Francisco Bay Area to give a sample Friday. A worker used a small tool to scrape her cheek, took three swabs of skin and asked her detailed questions about who she was looking for and their relationship.\u003c/p>\n\u003cp>The uncle’s landlord confirmed his house burned down with his vehicle still in the garage, but Quinones had no idea if any remains were found. Marbury’s name keeps going on and off the ever-changing list of the missing.\u003c/p>\n\u003cp>“I did it just to be proactive,” Quinones said Monday. “This is the one way I could contribute to helping find my uncle.”\u003c/p>\n\u003cp>Some of those who have given DNA came forward, like Quinones, after learning about the identification effort in their desperate search for a loved one, others after the sheriff’s office called to say that remains that probably belonged to a family member had been found.\u003c/p>\n\u003cp>Mattern declined to say Tuesday how many victims ANDE’s technology has helped identify. Sheriff Kory Honea’s office did not immediately respond to requests for comment.\u003c/p>\n\u003cp>The fire was 70 percent contained Tuesday. Rain in the forecast for Wednesday through Thanksgiving weekend could aid in fighting the fire but could also bring flash floods and complicate efforts to recover remains.\u003c/p>\n\u003cp>Once DNA is extracted from the remains, it is placed in a vial that goes into a black machine that looks like a bulky computer printer. It takes just two hours to process the material and get a DNA profile; traditional methods can take days or weeks. If a relative’s DNA is already in the system, a match will pop up right away.\u003c/p>\n\u003cp>Mattern said it has been surprisingly easy to get DNA from remains, despite the devastating damage done by the flames.\u003c/p>\n\u003cp>“We went in with pretty measured expectations, we didn’t know what we were walking into,” she said. “We have a tremendous database now of the victims of the fire.”\u003c/p>\n\u003cp>Ruth Dickover, director of the forensic science graduate program at the University of California-Davis, said that scientists have long been able to extract DNA from bone — a process that involves pulverizing the bone — but things can become more complicated if the remains of multiple people are mixed together.\u003c/p>\n\u003cp>“What’s left may not give you a nice beautiful profile,” she said.\u003cbr>\nANDE won a contract in 2009 to do research and development for federal agencies, and the company’s technology has been used in pilot programs for several years. Over the summer, it won FBI approval for use in accredited labs. Law enforcement agencies in Utah, New York and Miami have used the technology, as has the military.\u003c/p>\n\u003cp>This is the first time ANDE has helped identify victims after a natural disaster. The company has donated seven machines and about a dozen workers to the effort.\u003c/p>\n\u003cp>Sarah Warren drove an hour and a half from Redding on Monday to report her uncle, Devan Ruel, as missing. The sheriff’s office gave her a number to call about missing people, and when she called, she was told authorities would contact her if they needed her DNA, she said.\u003cbr>\nShe said no one told her about the collection desk at the old Sears, so she returned home without providing one.\u003c/p>\n\u003cp>“I could have done that so easily, just to be safe,” she said.\u003c/p>\n\u003cp>Warren hadn’t talked to Ruel in about eight years and said the family did not have an address for him.\u003c/p>\n\u003cp>“He was just an off-the-grid type of guy,” she said. “If he did perish that way it would be horrific. It deeply, deeply saddens me to even consider that being a possibility.”\u003c/p>\n\u003cp>Mattern said the sheriff’s office is looking for a way to make it easier for families who don’t live in Northern California to provide samples.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>And in hopes of easing fears that the DNA will be misused, the sheriff’s office and the company gave assurances it will be deleted once it is no longer needed.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/1934691/rapid-dna-analysis-used-to-help-id-camp-fire-victims","authors":["byline_science_1934691"],"categories":["science_30","science_35","science_39"],"tags":["science_3820","science_305","science_3370"],"featImg":"science_1934694","label":"science"},"science_219512":{"type":"posts","id":"science_219512","meta":{"index":"posts_1591205157","site":"science","id":"219512","score":null,"sort":[1441029611000]},"guestAuthors":[],"slug":"how-many-fish-in-the-sea-genetic-testing-could-answer-that","title":"How Many Fish in the Sea? Genetic Testing Could Answer That","publishDate":1441029611,"format":"image","headTitle":"How Many Fish in the Sea? Genetic Testing Could Answer That | KQED","labelTerm":{},"content":"\u003cp>Advances in genetic testing have revolutionized everything from health care decisions to crime forensics. Now, the technology may help protect marine life off the California coast.\u003c/p>\n\u003cp>In the waters of Monterey Bay, DNA sequencing is allowing biologists to study fish and whales without ever having seen them.\u003c/p>\n\u003cp>Just a sample of seawater, the volume of a water bottle, is enough to reveal what marine life has been swimming through that part of the ocean. The technique could improve marine monitoring, where scientists track an ecosystem year after year to gauge how it’s doing.\u003c/p>\n\u003cp>\u003cstrong>One Fish, Two Fish\u003c/strong>\u003c/p>\n\u003cp>Taking a marine census today requires hours of field time, either with scuba diving or boat trips.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>“It gets a little challenging because you’re floating, you’re swimming, you’re looking, you’re counting,” says diver Dan Abbott, unloading his scuba gear on a beach in Monterey.\u003c/p>\n\u003cp>He’s holding a waterproof clipboard, on which he’s tallied all the fish and marine life he saw in a kelp forest just offshore.\u003c/p>\n\u003cp>“About 150 fish in all. Pile perch, black perch, blue rockfish, kelp rockfish,” he says, just for a start. He’s diving with a team from \u003ca href=\"http://reefcheck.org/rcca/rcca_home.php\">Reef Check California\u003c/a>, a group of volunteers that surveys this site twice a year.\u003c/p>\n\u003cfigure id=\"attachment_219514\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/NPS.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-219514\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/NPS-800x455.jpg\" alt=\"Today, divers do marine surveys underwater, counting each organism they find.\" width=\"800\" height=\"455\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/NPS.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/NPS-400x228.jpg 400w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Today, divers do marine surveys underwater, counting each organism they find. \u003ccite>(National Park Service)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Listen to the story:\u003c/strong>\u003cbr>\nhttp://www.kqed.org/.stream/anon/radio/science/2015/08/20150831ScienceDNAmarinelife.mp3\u003cbr>\nThe group’s data help answer a question that’s key to California’s conservation efforts: are there more fish here now than there were eight years ago?\u003c/p>\n\u003cp>That’s when this kelp forest became part of a massive experiment to restore marine life in California. It was set aside as a \u003ca href=\"http://www.dfg.ca.gov/marine/mpa/index.asp\">marine protected area\u003c/a>, where there’s little or no fishing allowed.\u003c/p>\n\u003cp>There are now more than a hundred protected areas up and down the coast, covering 16 percent of state waters. The idea is that marine life will slowly recover there, improving the ecosystem both inside and outside the boundaries of each area.\u003c/p>\n\u003cp>The only way to know if these areas are working is through underwater surveys, repeated year after year. In 2013, \u003ca href=\"http://ww2.kqed.org/news/2013/02/28/california-ocean-reserves-show-promising-results-for-marine-life\">biologists reported encouraging results\u003c/a> in the protected areas off the Central Coast.\u003c/p>\n\u003cp>Field surveys are expensive. The state supplied $16 million for monitoring studies, and the funding has already run out in some regions of the coast. Monitoring has continued, thanks to universities, foundations and volunteer groups.\u003c/p>\n\u003cp>\u003cstrong>Studying the Ocean Without Getting Wet\u003c/strong>\u003c/p>\n\u003cp>“It’s been amazing what we can detect in just a liter of seawater,” says Jesse Port, an environmental genomicist at the Center for Ocean Solutions at Stanford University.\u003c/p>\n\u003cfigure id=\"attachment_219513\" class=\"wp-caption alignright\" style=\"max-width: 524px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/MBAQ.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\" wp-image-219513\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/MBAQ-800x563.jpg\" alt=\"Port first tested the DNA floating in the tanks at the Monterey Bay Aquarium.\" width=\"524\" height=\"369\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-800x563.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-400x282.jpg 400w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-1180x831.jpg 1180w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-960x676.jpg 960w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ.jpg 1200w\" sizes=\"(max-width: 524px) 100vw, 524px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Port first tested the DNA floating in the tanks at the Monterey Bay Aquarium. Can you guess why he found turkey DNA in the tanks? \u003ccite>(Lauren Sommer/KQED)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>He points to a rack of one-liter Nalgene water bottles that he uses to take seawater samples from the kelp forests in Monterey Bay. The rest of the work happens in the lab with a technique known as “environmental DNA” or eDNA.\u003c/p>\n\u003cp>“So all organisms shed their DNA,” he says. “Their skin, their scales, their waste – all of this gets into the water. You can think of it as a soup of genetic information.”\u003c/p>\n\u003cp>Port filters the seawater to collect all the cells. Then, he weeds out the algae and plankton and sequences the DNA of all the vertebrates, like whales, seals, and fish.\u003c/p>\n\u003cp>“We get, with the machine we’re using, 150 million sequence reads for a given sequence run,” he says, “and that’s a lot of information.”\u003c/p>\n\u003cp>Those gigabytes of results require heavy data-crunching, but eventually, he ends up with a spreadsheet that tells him what organisms were found.\u003c/p>\n\u003cp>The approach is possible because DNA sequencing has gotten so much cheaper. One sample costs just $1,500.\u003c/p>\n\u003cp>“This was just not possible five, ten years ago,” Port says. “And sequencing technology is just going to get better, so this will probably get even cheaper.”\u003c/p>\n\u003cp>\u003cstrong>Finding Turkey Underwater\u003c/strong>\u003c/p>\n\u003cp>Port first ran DNA tests in one of the large tanks at the Monterey Bay Aquarium, which provided an easy test case because he knew exactly what was swimming there.\u003c/p>\n\u003cp>But he got back results he didn’t quite believe. “Things like turkey,” he says. “We picked up chicken DNA in these tanks.”\u003c/p>\n\u003caside class=\"pullquote alignright\">“This is going to be transformative in oceanography. You don’t have to be out there on a boat with a huge crew, spending all this money.”\u003ccite>Jim Birch,\u003cbr>Monterey Bay Aquarium Research Institute\u003c/cite>\u003c/aside>\n\u003cp>Turns out, poultry was in the feed some of the fish were getting. But it raised some big questions. How do you know whether the DNA comes from a fish or from something it ate miles away? Or how do you know the DNA didn’t float in on a current?\u003c/p>\n\u003cp>Port is still working on the answers to these questions and he’s doing studies to ground truth his results, checking them against what scuba divers find. But if the technology proves itself in the ocean, it could revolutionize how marine monitoring is done.\u003c/p>\n\u003cp>“You can cover such a larger area by taking water samples,” he says, “rather than having divers do that all themselves.”\u003c/p>\n\u003cp>Paul Michel, the superintendent of the Monterey Bay National Marine Sanctuary, says they’re already using eDNA testing to help assess species diversity in the sanctuary.\u003c/p>\n\u003cp>“Absolutely, we did DNA testing on a research cruise in May,” Michel says, “and at each stop on the way, we were taking water samples. We can compare the DNA results to other types of samples over time.”\u003c/p>\n\u003cp>Eventually, it doesn’t even have to be humans taking those water samples.\u003c/p>\n\u003cfigure id=\"attachment_219519\" class=\"wp-caption alignright\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/lrauv_mission3.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-219519\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/lrauv_mission3-800x487.jpg\" alt=\"MBARI's long-range autonomous underwater vehicle can remain at sea, unattended, for weeks at a time.\" width=\"800\" height=\"487\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-800x487.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-400x243.jpg 400w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1440x876.jpg 1440w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1920x1168.jpg 1920w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1180x718.jpg 1180w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-960x584.jpg 960w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3.jpg 2034w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">MBARI’s long-range autonomous underwater vehicle can take samples at sea, unattended, for weeks at a time. \u003ccite>(Todd Walsh (c) 2010 MBARI)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>DNA Lab at Sea\u003c/strong>\u003c/p>\n\u003cp>“What this is, is a microbiology lab that exists out in the ocean,” says Jim Birch of the Monterey Bay Aquarium Research Institute, pointing to a 10-foot yellow tube. It’s called a long-range AUV, or autonomous underwater vehicle.\u003c/p>\n\u003cp>It looks like a torpedo, but it’s actually a robot, containing a miniature DNA lab called an \u003ca href=\"http://www.mbari.org/esp/\">Environmental Sample Processor\u003c/a>.\u003c/p>\n\u003cp>The robot cruises along underwater, taking samples and analyzing them onboard. Birch recently sent it out for a test run in Monterey Bay.\u003c/p>\n\u003cp>“I was sitting in my living room with my computer open and there in front of me was the control panel for the AUV,” he says. “And I could direct it to go to a new place and it was just this surreal feeling.”\u003c/p>\n\u003cp>When the AUV finds an organism it’s looking for, it surfaces and calls home, pinging a satellite or cell phone network with the data, and giving scientists an almost real-time snapshot of the ocean.\u003c/p>\n\u003cp>Currently, it only tests for one thing at a time, like algae or plankton, and Birch says there’s more engineering work to be done before the AUV gains widespread use.\u003c/p>\n\u003cp>“This is going to be transformative in oceanography,” he says. “You don’t have to be out there on a boat with a huge crew, spending all this money.”\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>A change that could help the state’s conservation funding go farther, ensuring California’s marine protected areas are working.\u003c/p>\n\n","blocks":[],"excerpt":"DNA testing, the same tech used in human health, could change the way biologists study the ocean.","status":"publish","parent":0,"modified":1704931366,"stats":{"hasAudio":true,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":42,"wordCount":1309},"headData":{"title":"How Many Fish in the Sea? Genetic Testing Could Answer That | KQED","description":"DNA testing, the same tech used in human health, could change the way biologists study the ocean.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"source":"KQED Science","sourceUrl":"https://ww2.kqed.org/science/","sticky":false,"path":"/science/219512/how-many-fish-in-the-sea-genetic-testing-could-answer-that","audioUrl":"http://www.kqed.org/.stream/anon/radio/science/2015/08/20150831ScienceDNAmarinelife.mp3","audioDuration":null,"audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>Advances in genetic testing have revolutionized everything from health care decisions to crime forensics. Now, the technology may help protect marine life off the California coast.\u003c/p>\n\u003cp>In the waters of Monterey Bay, DNA sequencing is allowing biologists to study fish and whales without ever having seen them.\u003c/p>\n\u003cp>Just a sample of seawater, the volume of a water bottle, is enough to reveal what marine life has been swimming through that part of the ocean. The technique could improve marine monitoring, where scientists track an ecosystem year after year to gauge how it’s doing.\u003c/p>\n\u003cp>\u003cstrong>One Fish, Two Fish\u003c/strong>\u003c/p>\n\u003cp>Taking a marine census today requires hours of field time, either with scuba diving or boat trips.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“It gets a little challenging because you’re floating, you’re swimming, you’re looking, you’re counting,” says diver Dan Abbott, unloading his scuba gear on a beach in Monterey.\u003c/p>\n\u003cp>He’s holding a waterproof clipboard, on which he’s tallied all the fish and marine life he saw in a kelp forest just offshore.\u003c/p>\n\u003cp>“About 150 fish in all. Pile perch, black perch, blue rockfish, kelp rockfish,” he says, just for a start. He’s diving with a team from \u003ca href=\"http://reefcheck.org/rcca/rcca_home.php\">Reef Check California\u003c/a>, a group of volunteers that surveys this site twice a year.\u003c/p>\n\u003cfigure id=\"attachment_219514\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/NPS.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-219514\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/NPS-800x455.jpg\" alt=\"Today, divers do marine surveys underwater, counting each organism they find.\" width=\"800\" height=\"455\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/NPS.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/NPS-400x228.jpg 400w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Today, divers do marine surveys underwater, counting each organism they find. \u003ccite>(National Park Service)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>Listen to the story:\u003c/strong>\u003cbr>\nhttp://www.kqed.org/.stream/anon/radio/science/2015/08/20150831ScienceDNAmarinelife.mp3\u003cbr>\nThe group’s data help answer a question that’s key to California’s conservation efforts: are there more fish here now than there were eight years ago?\u003c/p>\n\u003cp>That’s when this kelp forest became part of a massive experiment to restore marine life in California. It was set aside as a \u003ca href=\"http://www.dfg.ca.gov/marine/mpa/index.asp\">marine protected area\u003c/a>, where there’s little or no fishing allowed.\u003c/p>\n\u003cp>There are now more than a hundred protected areas up and down the coast, covering 16 percent of state waters. The idea is that marine life will slowly recover there, improving the ecosystem both inside and outside the boundaries of each area.\u003c/p>\n\u003cp>The only way to know if these areas are working is through underwater surveys, repeated year after year. In 2013, \u003ca href=\"http://ww2.kqed.org/news/2013/02/28/california-ocean-reserves-show-promising-results-for-marine-life\">biologists reported encouraging results\u003c/a> in the protected areas off the Central Coast.\u003c/p>\n\u003cp>Field surveys are expensive. The state supplied $16 million for monitoring studies, and the funding has already run out in some regions of the coast. Monitoring has continued, thanks to universities, foundations and volunteer groups.\u003c/p>\n\u003cp>\u003cstrong>Studying the Ocean Without Getting Wet\u003c/strong>\u003c/p>\n\u003cp>“It’s been amazing what we can detect in just a liter of seawater,” says Jesse Port, an environmental genomicist at the Center for Ocean Solutions at Stanford University.\u003c/p>\n\u003cfigure id=\"attachment_219513\" class=\"wp-caption alignright\" style=\"max-width: 524px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/MBAQ.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\" wp-image-219513\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/MBAQ-800x563.jpg\" alt=\"Port first tested the DNA floating in the tanks at the Monterey Bay Aquarium.\" width=\"524\" height=\"369\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-800x563.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-400x282.jpg 400w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-1180x831.jpg 1180w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ-960x676.jpg 960w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/MBAQ.jpg 1200w\" sizes=\"(max-width: 524px) 100vw, 524px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Port first tested the DNA floating in the tanks at the Monterey Bay Aquarium. Can you guess why he found turkey DNA in the tanks? \u003ccite>(Lauren Sommer/KQED)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>He points to a rack of one-liter Nalgene water bottles that he uses to take seawater samples from the kelp forests in Monterey Bay. The rest of the work happens in the lab with a technique known as “environmental DNA” or eDNA.\u003c/p>\n\u003cp>“So all organisms shed their DNA,” he says. “Their skin, their scales, their waste – all of this gets into the water. You can think of it as a soup of genetic information.”\u003c/p>\n\u003cp>Port filters the seawater to collect all the cells. Then, he weeds out the algae and plankton and sequences the DNA of all the vertebrates, like whales, seals, and fish.\u003c/p>\n\u003cp>“We get, with the machine we’re using, 150 million sequence reads for a given sequence run,” he says, “and that’s a lot of information.”\u003c/p>\n\u003cp>Those gigabytes of results require heavy data-crunching, but eventually, he ends up with a spreadsheet that tells him what organisms were found.\u003c/p>\n\u003cp>The approach is possible because DNA sequencing has gotten so much cheaper. One sample costs just $1,500.\u003c/p>\n\u003cp>“This was just not possible five, ten years ago,” Port says. “And sequencing technology is just going to get better, so this will probably get even cheaper.”\u003c/p>\n\u003cp>\u003cstrong>Finding Turkey Underwater\u003c/strong>\u003c/p>\n\u003cp>Port first ran DNA tests in one of the large tanks at the Monterey Bay Aquarium, which provided an easy test case because he knew exactly what was swimming there.\u003c/p>\n\u003cp>But he got back results he didn’t quite believe. “Things like turkey,” he says. “We picked up chicken DNA in these tanks.”\u003c/p>\n\u003caside class=\"pullquote alignright\">“This is going to be transformative in oceanography. You don’t have to be out there on a boat with a huge crew, spending all this money.”\u003ccite>Jim Birch,\u003cbr>Monterey Bay Aquarium Research Institute\u003c/cite>\u003c/aside>\n\u003cp>Turns out, poultry was in the feed some of the fish were getting. But it raised some big questions. How do you know whether the DNA comes from a fish or from something it ate miles away? Or how do you know the DNA didn’t float in on a current?\u003c/p>\n\u003cp>Port is still working on the answers to these questions and he’s doing studies to ground truth his results, checking them against what scuba divers find. But if the technology proves itself in the ocean, it could revolutionize how marine monitoring is done.\u003c/p>\n\u003cp>“You can cover such a larger area by taking water samples,” he says, “rather than having divers do that all themselves.”\u003c/p>\n\u003cp>Paul Michel, the superintendent of the Monterey Bay National Marine Sanctuary, says they’re already using eDNA testing to help assess species diversity in the sanctuary.\u003c/p>\n\u003cp>“Absolutely, we did DNA testing on a research cruise in May,” Michel says, “and at each stop on the way, we were taking water samples. We can compare the DNA results to other types of samples over time.”\u003c/p>\n\u003cp>Eventually, it doesn’t even have to be humans taking those water samples.\u003c/p>\n\u003cfigure id=\"attachment_219519\" class=\"wp-caption alignright\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/lrauv_mission3.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-219519\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/08/lrauv_mission3-800x487.jpg\" alt=\"MBARI's long-range autonomous underwater vehicle can remain at sea, unattended, for weeks at a time.\" width=\"800\" height=\"487\" srcset=\"https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-800x487.jpg 800w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-400x243.jpg 400w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1440x876.jpg 1440w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1920x1168.jpg 1920w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-1180x718.jpg 1180w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3-960x584.jpg 960w, https://cdn.kqed.org/wp-content/uploads/sites/35/2015/08/lrauv_mission3.jpg 2034w\" sizes=\"(max-width: 800px) 100vw, 800px\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">MBARI’s long-range autonomous underwater vehicle can take samples at sea, unattended, for weeks at a time. \u003ccite>(Todd Walsh (c) 2010 MBARI)\u003c/cite>\u003c/figcaption>\u003c/figure>\n\u003cp>\u003cstrong>DNA Lab at Sea\u003c/strong>\u003c/p>\n\u003cp>“What this is, is a microbiology lab that exists out in the ocean,” says Jim Birch of the Monterey Bay Aquarium Research Institute, pointing to a 10-foot yellow tube. It’s called a long-range AUV, or autonomous underwater vehicle.\u003c/p>\n\u003cp>It looks like a torpedo, but it’s actually a robot, containing a miniature DNA lab called an \u003ca href=\"http://www.mbari.org/esp/\">Environmental Sample Processor\u003c/a>.\u003c/p>\n\u003cp>The robot cruises along underwater, taking samples and analyzing them onboard. Birch recently sent it out for a test run in Monterey Bay.\u003c/p>\n\u003cp>“I was sitting in my living room with my computer open and there in front of me was the control panel for the AUV,” he says. “And I could direct it to go to a new place and it was just this surreal feeling.”\u003c/p>\n\u003cp>When the AUV finds an organism it’s looking for, it surfaces and calls home, pinging a satellite or cell phone network with the data, and giving scientists an almost real-time snapshot of the ocean.\u003c/p>\n\u003cp>Currently, it only tests for one thing at a time, like algae or plankton, and Birch says there’s more engineering work to be done before the AUV gains widespread use.\u003c/p>\n\u003cp>“This is going to be transformative in oceanography,” he says. “You don’t have to be out there on a boat with a huge crew, spending all this money.”\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>A change that could help the state’s conservation funding go farther, ensuring California’s marine protected areas are working.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/219512/how-many-fish-in-the-sea-genetic-testing-could-answer-that","authors":["239"],"series":["science_2625"],"categories":["science_46","science_2631","science_30","science_29","science_35","science_40"],"tags":["science_305","science_268"],"featImg":"science_221206","label":"source_science_219512"},"science_27205":{"type":"posts","id":"science_27205","meta":{"index":"posts_1591205157","site":"science","id":"27205","score":null,"sort":[1424710856000]},"guestAuthors":[],"slug":"scientists-create-the-most-precise-3d-map-of-the-human-genome-yet","title":"Scientists Create the Most Precise 3D Map of the Human Genome Yet","publishDate":1424710856,"format":"aside","headTitle":"Scientists Create the Most Precise 3D Map of the Human Genome Yet | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_27218\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/Nucleome.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-27218\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/Nucleome.jpg\" alt=\"The human genome is packaged into a series of loops. This representation is from the Genome: Unlocking Life's Code exhibition, currently at The Tech Museum in San Jose. Each color represents a separate chromosome. \" width=\"800\" height=\"469\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The human genome is packaged into a series of loops. This representation is from the \u003ca href=\"http://www.thetech.org/genome\">Genome: Unlocking Life’s Code\u003c/a> exhibition, currently at \u003ca href=\"http://www.thetech.org/\">The Tech Museum\u003c/a> in San Jose. Each color represents a separate chromosome. (The Tech Museum)\u003c/figcaption>\u003c/figure>\n\u003cp>Most people know our genetic code involves the letters A, T, C and G (adenine, thymine, guanine and cytosine) to make up DNA. But what fewer people know about is the code found in the packaging of DNA. And there is a lot of it there.\u003c/p>\n\u003cp>Until recently, we didn’t have a good way to systematically get at that information. Science took a big step forward in being able to do this with the \u003ca href=\"http://www.cell.com/cell/abstract/S0092-8674(14)01497-4\">publication of the most precise map to date\u003c/a> of how human cells organize their 6 feet of DNA into their nuclei, a space that has a diameter of only around 0.0000016 inches. This kind of map will not only tell us how the instructions in our DNA lead to making each one of us, but it may also provide new ways to understand and even treat diseases like cancer.\u003c/p>\n\u003cp>In this study, Baylor College of Medicine researcher Suhas Rao and coworkers focused on a part of nuclear organization called DNA loops. Basically, our DNA forms a set of loops that each act as an independent region. Each loop has a set of controls for genes in that loop that don’t affect genes outside of that loop.\u003c/p>\n\u003cp>One of the most surprising results of this study was that instead of the one million loops that many scientists expected, the authors found only around 10,000 of them. Not simple to study but definitely a more manageable number than one million!\u003c/p>\n\u003cp>One way to think about these results is that it is a bit like the original human genome project. Just like that original DNA sequence, it is providing us with a reference to which all other studies like this can be compared.\u003c/p>\n\u003cfigure id=\"attachment_27220\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/BreastCancer.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-27220\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/BreastCancer.jpg\" alt=\"Understanding how DNA is packaged may help us understand why certain mutations can cause cancers. (Wikimedia Commons)\" width=\"320\" height=\"213\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Understanding how DNA is packaged may help us understand why certain mutations can cause cancers. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Breast_cancer_cells_(1).jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Scientists will be able to, for example, determine how DNA is packaged in the cells of people with certain diseases and compare it to this reference map. From that comparison they may be able to better understand why a certain DNA change leads to a certain disease.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>This matters because many of the DNA differences scientists are discovering that are important in human disease happen outside of the 2 percent of DNA that comprise our genes. This makes it very hard to know why a DNA change is causing a certain problem. And if we don’t know the reasoning, it is hard to come up with a treatment for that disease.\u003c/p>\n\u003cp>Most likely many of these DNA differences affect how a piece of DNA controls a gene but it has proven very tricky to connect the gene to the DNA difference. This becomes much easier with the mapping of DNA loops.\u003c/p>\n\u003cp>In fact, this sort of map has been deemed so important that the \u003ca href=\"http://www.nih.gov/\">National Institutes of Health\u003c/a> has launched a new initiative called the \u003ca href=\"http://commonfund.nih.gov/4Dnucleome/index\">4D Nucleome project\u003c/a> which will create even more detailed maps. The project will involve many researchers all working together to map the 3D structure of the genome in a wide variety of healthy and diseased cell types over time. (Time is the 4\u003csup>th\u003c/sup> dimension in 4D.)\u003c/p>\n\u003cp>\u003cstrong>Linking DNA Differences to Genes \u003c/strong>\u003c/p>\n\u003cp>Most people have heard of genes, those stretches of DNA that each have the instructions for one small part of us. But as scientists have known for quite a while, this 2 percent of our DNA is not the whole story of our genome. The other 98 percent plays an important role in determining when and where a gene should be on and to what level.\u003c/p>\n\u003cp>One way that genes are controlled is with short DNA sequences called enhancers. These enhancers turn on genes in some cells and not in others.\u003c/p>\n\u003cp>What has been hard to understand with these enhancers is how they know which genes to turn on and which ones to leave alone. In the bacterial world it is easy…the equivalent of an enhancer turns on whatever gene is closest. The same is not true in eukaryotes like us.\u003c/p>\n\u003cp>Enhancers sometimes ignore genes that are closest to them and instead activate a set of genes that is much further away. It turns out that one way they are able to pull this off is by only working within their own DNA loop.\u003c/p>\n\u003cp>So imagine a bit of DNA that turns on many nearby genes. We will call it ENH for an enhancer.\u003c/p>\n\u003cp>Now let’s imagine that a gene that can cause cancer when it is turned on is in a nearby loop. This gene might have been important during development when an embryo was becoming an infant, but it is now dangerous and so is tucked away in a place where it stays off. The situation looks something like this:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/TwoDNAloops.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-27208\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/TwoDNAloops.jpg\" alt=\"TwoDNAloops\" width=\"394\" height=\"223\">\u003c/a>\u003c/p>\n\u003cp>Since the enhancer is in a different loop, it doesn’t affect this gene. The gene stays safely off.\u003c/p>\n\u003cp>Now imagine something has happened, perhaps a mutation, that leads to a different DNA loop pattern. Here is the new situation:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/OneDNAloop.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-27209\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/OneDNAloop.jpg\" alt=\"OneDNAloop\" width=\"394\" height=\"219\">\u003c/a>\u003c/p>\n\u003cp>The two loops have merged into one big loop. Now the enhancer can turn on the gene causing cancer.\u003c/p>\n\u003cp>This would be very hard to figure out without a map like this. The mutation that caused it isn’t in the enhancer or in the gene itself. It is somewhere else that affected how the DNA in the cell was looped.\u003c/p>\n\u003cp>It is for situations like this that precise 3D maps of the human genome will prove to be so useful. And of course, science isn’t just about curing disease.\u003c/p>\n\u003cp>Maps like these will also help us understand why different kinds of cells look and act differently even though they all share the exact same DNA. Or how a single cell develops into the trillions that make up a human. Or about a million other cool things.\u003c/p>\n\u003cp>The following short video is a great way to learn what else Rao and coworkers learned in this study about human DNA:\u003c/p>\n\u003cp>http://www.youtube.com/watch?v=dES-ozV65u4\u003c/p>\n\u003cp> \u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.thetech.org/\">The Tech Museum of Innovation\u003c/a> is hosting a traveling exhibition from the Smithsonian, \u003ca href=\"http://www.thetech.org/genome\">Genome: Unlocking Life’s Code\u003c/a> until April 27, 2015. Come and see it to learn more about what that original human genome project has allowed us to learn about ourselves over the past decade or so.\u003c/em>\u003c/p>\n\n","blocks":[],"excerpt":"Until recently scientists have not been able to figure out the information coded in the folding of our DNA in the nucleus. A new map now makes this task simpler. This kind of map will not only tell us how the instructions in our DNA lead to making each one of us, but it may also provide new ways to understand and even treat diseases like cancer.","status":"publish","parent":0,"modified":1704932233,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":28,"wordCount":1107},"headData":{"title":"Scientists Create the Most Precise 3D Map of the Human Genome Yet | KQED","description":"Until recently scientists have not been able to figure out the information coded in the folding of our DNA in the nucleus. A new map now makes this task simpler. This kind of map will not only tell us how the instructions in our DNA lead to making each one of us, but it may also provide new ways to understand and even treat diseases like cancer.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"path":"/science/27205/scientists-create-the-most-precise-3d-map-of-the-human-genome-yet","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_27218\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/Nucleome.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-27218\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/Nucleome.jpg\" alt=\"The human genome is packaged into a series of loops. This representation is from the Genome: Unlocking Life's Code exhibition, currently at The Tech Museum in San Jose. Each color represents a separate chromosome. \" width=\"800\" height=\"469\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The human genome is packaged into a series of loops. This representation is from the \u003ca href=\"http://www.thetech.org/genome\">Genome: Unlocking Life’s Code\u003c/a> exhibition, currently at \u003ca href=\"http://www.thetech.org/\">The Tech Museum\u003c/a> in San Jose. Each color represents a separate chromosome. (The Tech Museum)\u003c/figcaption>\u003c/figure>\n\u003cp>Most people know our genetic code involves the letters A, T, C and G (adenine, thymine, guanine and cytosine) to make up DNA. But what fewer people know about is the code found in the packaging of DNA. And there is a lot of it there.\u003c/p>\n\u003cp>Until recently, we didn’t have a good way to systematically get at that information. Science took a big step forward in being able to do this with the \u003ca href=\"http://www.cell.com/cell/abstract/S0092-8674(14)01497-4\">publication of the most precise map to date\u003c/a> of how human cells organize their 6 feet of DNA into their nuclei, a space that has a diameter of only around 0.0000016 inches. This kind of map will not only tell us how the instructions in our DNA lead to making each one of us, but it may also provide new ways to understand and even treat diseases like cancer.\u003c/p>\n\u003cp>In this study, Baylor College of Medicine researcher Suhas Rao and coworkers focused on a part of nuclear organization called DNA loops. Basically, our DNA forms a set of loops that each act as an independent region. Each loop has a set of controls for genes in that loop that don’t affect genes outside of that loop.\u003c/p>\n\u003cp>One of the most surprising results of this study was that instead of the one million loops that many scientists expected, the authors found only around 10,000 of them. Not simple to study but definitely a more manageable number than one million!\u003c/p>\n\u003cp>One way to think about these results is that it is a bit like the original human genome project. Just like that original DNA sequence, it is providing us with a reference to which all other studies like this can be compared.\u003c/p>\n\u003cfigure id=\"attachment_27220\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/BreastCancer.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-27220\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/BreastCancer.jpg\" alt=\"Understanding how DNA is packaged may help us understand why certain mutations can cause cancers. (Wikimedia Commons)\" width=\"320\" height=\"213\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Understanding how DNA is packaged may help us understand why certain mutations can cause cancers. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Breast_cancer_cells_(1).jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Scientists will be able to, for example, determine how DNA is packaged in the cells of people with certain diseases and compare it to this reference map. From that comparison they may be able to better understand why a certain DNA change leads to a certain disease.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>This matters because many of the DNA differences scientists are discovering that are important in human disease happen outside of the 2 percent of DNA that comprise our genes. This makes it very hard to know why a DNA change is causing a certain problem. And if we don’t know the reasoning, it is hard to come up with a treatment for that disease.\u003c/p>\n\u003cp>Most likely many of these DNA differences affect how a piece of DNA controls a gene but it has proven very tricky to connect the gene to the DNA difference. This becomes much easier with the mapping of DNA loops.\u003c/p>\n\u003cp>In fact, this sort of map has been deemed so important that the \u003ca href=\"http://www.nih.gov/\">National Institutes of Health\u003c/a> has launched a new initiative called the \u003ca href=\"http://commonfund.nih.gov/4Dnucleome/index\">4D Nucleome project\u003c/a> which will create even more detailed maps. The project will involve many researchers all working together to map the 3D structure of the genome in a wide variety of healthy and diseased cell types over time. (Time is the 4\u003csup>th\u003c/sup> dimension in 4D.)\u003c/p>\n\u003cp>\u003cstrong>Linking DNA Differences to Genes \u003c/strong>\u003c/p>\n\u003cp>Most people have heard of genes, those stretches of DNA that each have the instructions for one small part of us. But as scientists have known for quite a while, this 2 percent of our DNA is not the whole story of our genome. The other 98 percent plays an important role in determining when and where a gene should be on and to what level.\u003c/p>\n\u003cp>One way that genes are controlled is with short DNA sequences called enhancers. These enhancers turn on genes in some cells and not in others.\u003c/p>\n\u003cp>What has been hard to understand with these enhancers is how they know which genes to turn on and which ones to leave alone. In the bacterial world it is easy…the equivalent of an enhancer turns on whatever gene is closest. The same is not true in eukaryotes like us.\u003c/p>\n\u003cp>Enhancers sometimes ignore genes that are closest to them and instead activate a set of genes that is much further away. It turns out that one way they are able to pull this off is by only working within their own DNA loop.\u003c/p>\n\u003cp>So imagine a bit of DNA that turns on many nearby genes. We will call it ENH for an enhancer.\u003c/p>\n\u003cp>Now let’s imagine that a gene that can cause cancer when it is turned on is in a nearby loop. This gene might have been important during development when an embryo was becoming an infant, but it is now dangerous and so is tucked away in a place where it stays off. The situation looks something like this:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/TwoDNAloops.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-27208\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/TwoDNAloops.jpg\" alt=\"TwoDNAloops\" width=\"394\" height=\"223\">\u003c/a>\u003c/p>\n\u003cp>Since the enhancer is in a different loop, it doesn’t affect this gene. The gene stays safely off.\u003c/p>\n\u003cp>Now imagine something has happened, perhaps a mutation, that leads to a different DNA loop pattern. Here is the new situation:\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/OneDNAloop.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-27209\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/02/OneDNAloop.jpg\" alt=\"OneDNAloop\" width=\"394\" height=\"219\">\u003c/a>\u003c/p>\n\u003cp>The two loops have merged into one big loop. Now the enhancer can turn on the gene causing cancer.\u003c/p>\n\u003cp>This would be very hard to figure out without a map like this. The mutation that caused it isn’t in the enhancer or in the gene itself. It is somewhere else that affected how the DNA in the cell was looped.\u003c/p>\n\u003cp>It is for situations like this that precise 3D maps of the human genome will prove to be so useful. And of course, science isn’t just about curing disease.\u003c/p>\n\u003cp>Maps like these will also help us understand why different kinds of cells look and act differently even though they all share the exact same DNA. Or how a single cell develops into the trillions that make up a human. Or about a million other cool things.\u003c/p>\n\u003cp>The following short video is a great way to learn what else Rao and coworkers learned in this study about human DNA:\u003c/p>\u003c/p>\u003cp>\u003cspan class='utils-parseShortcode-shortcodes-__youtubeShortcode__embedYoutube'>\n \u003cspan class='utils-parseShortcode-shortcodes-__youtubeShortcode__embedYoutubeInside'>\n \u003ciframe\n loading='lazy'\n class='utils-parseShortcode-shortcodes-__youtubeShortcode__youtubePlayer'\n type='text/html'\n src='//www.youtube.com/embed/dES-ozV65u4'\n title='//www.youtube.com/embed/dES-ozV65u4'\n allowfullscreen='true'\n style='border:0;'>\u003c/iframe>\n \u003c/span>\n \u003c/span>\u003c/p>\u003cp>\u003cp> \u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cem>\u003ca href=\"http://www.thetech.org/\">The Tech Museum of Innovation\u003c/a> is hosting a traveling exhibition from the Smithsonian, \u003ca href=\"http://www.thetech.org/genome\">Genome: Unlocking Life’s Code\u003c/a> until April 27, 2015. Come and see it to learn more about what that original human genome project has allowed us to learn about ourselves over the past decade or so.\u003c/em>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/27205/scientists-create-the-most-precise-3d-map-of-the-human-genome-yet","authors":["6177"],"categories":["science_30","science_39"],"tags":["science_305"],"featImg":"science_27218","label":"science"},"science_26186":{"type":"posts","id":"science_26186","meta":{"index":"posts_1591205157","site":"science","id":"26186","score":null,"sort":[1421116209000]},"guestAuthors":[],"slug":"23andme-strikes-another-deal-with-big-pharma","title":"23andMe Strikes Another Deal With Big Pharma","publishDate":1421116209,"format":"aside","headTitle":"23andMe Strikes Another Deal With Big Pharma | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_26269\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/23andMe_Box-e1421263543823.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"wp-image-26269 size-full\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/23andMe_Box-e1421263543823.jpg\" alt=\"\" width=\"640\" height=\"364\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">23andMe sells genetic testing kits and has recently started sharing that data with pharmaceutical companies. (23andMe)\u003c/figcaption>\u003c/figure>\n\u003cp>It hasn’t taken long for \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>, the Mountain View-based genetics company, to strike another deal with big pharma.\u003c/p>\n\u003cp>Last week, the Google-backed firm announced a $60 million agreement to allow Genentech to use participant data to study Parkinson’s disease. A new agreement announced Monday will give Pfizer access to 5,000 people in the company’s database to study the genetics of lupus.\u003c/p>\n\u003cp>It could be a new way to come up with treatments, says Emily Drabant Conley, Director of Business Development.\u003c/p>\n\u003cp>“We’re quite hopeful that the information is being leveraged to move us toward therapies and cures,” Drabant Conley says.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘We’re quite hopeful that the information is being leveraged to move us toward therapies and cures.’\u003ccite>— Emily Drabant Conley,\u003cbr>\n23andMe Director of Business Development\u003c/cite>\u003c/aside>\n\u003cp>The biotech firm sells $99 personal DNA kits that, through one dab of saliva, can tell consumers about their genetic make-up and ancestry. It has enrolled more than 800,000 participants and 650,000 of those have consented to share their medical information.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>“Not only are they benefiting by learning about themselves,” says Drabant Conley, “but when they consent to participate in research it gives us the ability to go back to them repeatedly over time and collect more info and engage them in the research that our partners are doing.”\u003c/p>\n\u003cp>Critics say the company is making millions by selling its users’ data. Concerns include privacy breaches and whether insurance companies would increase rates if they had access to a member’s genetic history.\u003c/p>\n\u003cp>23andMe came under attack in 2013 when the Food and Drug Administration issued a \u003ca href=\"http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm\">warning letter\u003c/a> saying the company was marketing genetic health analyses without approval, and raising concerns about the accuracy of the tests and the health risks to consumers of inaccurate tests.\u003c/p>\n\u003cp>A 23andMe \u003ca href=\"http://www.ispot.tv/ad/7qoF/23-and-me\">television commercial\u003c/a> at the time said people could discover if they “might have an increased risk of heart disease, arthritis, gallstones, [or] hemochromatosis.” 23andMe also gave people an analysis of genetic markers it said were associated with 254 specific diseases and conditions.\u003c/p>\n\u003cp>Concerned about “the public health consequences of inaccurate results,” the FDA asked company founder Anne Wojcicki to stop marketing the health analyses until the “diagnostic and prognostic capability of genomic information has been clinically validated.”\u003c/p>\n\u003cp>23andMe has \u003ca href=\"http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/ucm391016.htm\">stopped marketing\u003c/a> the health analyses in the U.S., but is \u003ca href=\"http://blog.23andme.com/news/update-on-the-regulatory-review-process-with-the-fda/\">working with the FDA\u003c/a> to develop protocols that will allow the company to resume that part of its business.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>23andMe is expected to announce another ten partnerships with pharmaceutical companies over the next several weeks.\u003c/p>\n\n","blocks":[],"excerpt":"The Mountain View-based company will sell genetic information to Pfizer for a study into the genetic markers for lupus. ","status":"publish","parent":0,"modified":1704932410,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":14,"wordCount":483},"headData":{"title":"23andMe Strikes Another Deal With Big Pharma | KQED","description":"The Mountain View-based company will sell genetic information to Pfizer for a study into the genetic markers for lupus. ","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"path":"/science/26186/23andme-strikes-another-deal-with-big-pharma","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_26269\" class=\"wp-caption alignleft\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/23andMe_Box-e1421263543823.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"wp-image-26269 size-full\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/23andMe_Box-e1421263543823.jpg\" alt=\"\" width=\"640\" height=\"364\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">23andMe sells genetic testing kits and has recently started sharing that data with pharmaceutical companies. (23andMe)\u003c/figcaption>\u003c/figure>\n\u003cp>It hasn’t taken long for \u003ca href=\"https://www.23andme.com/\">23andMe\u003c/a>, the Mountain View-based genetics company, to strike another deal with big pharma.\u003c/p>\n\u003cp>Last week, the Google-backed firm announced a $60 million agreement to allow Genentech to use participant data to study Parkinson’s disease. A new agreement announced Monday will give Pfizer access to 5,000 people in the company’s database to study the genetics of lupus.\u003c/p>\n\u003cp>It could be a new way to come up with treatments, says Emily Drabant Conley, Director of Business Development.\u003c/p>\n\u003cp>“We’re quite hopeful that the information is being leveraged to move us toward therapies and cures,” Drabant Conley says.\u003c/p>\n\u003caside class=\"pullquote alignleft\">‘We’re quite hopeful that the information is being leveraged to move us toward therapies and cures.’\u003ccite>— Emily Drabant Conley,\u003cbr>\n23andMe Director of Business Development\u003c/cite>\u003c/aside>\n\u003cp>The biotech firm sells $99 personal DNA kits that, through one dab of saliva, can tell consumers about their genetic make-up and ancestry. It has enrolled more than 800,000 participants and 650,000 of those have consented to share their medical information.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“Not only are they benefiting by learning about themselves,” says Drabant Conley, “but when they consent to participate in research it gives us the ability to go back to them repeatedly over time and collect more info and engage them in the research that our partners are doing.”\u003c/p>\n\u003cp>Critics say the company is making millions by selling its users’ data. Concerns include privacy breaches and whether insurance companies would increase rates if they had access to a member’s genetic history.\u003c/p>\n\u003cp>23andMe came under attack in 2013 when the Food and Drug Administration issued a \u003ca href=\"http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm\">warning letter\u003c/a> saying the company was marketing genetic health analyses without approval, and raising concerns about the accuracy of the tests and the health risks to consumers of inaccurate tests.\u003c/p>\n\u003cp>A 23andMe \u003ca href=\"http://www.ispot.tv/ad/7qoF/23-and-me\">television commercial\u003c/a> at the time said people could discover if they “might have an increased risk of heart disease, arthritis, gallstones, [or] hemochromatosis.” 23andMe also gave people an analysis of genetic markers it said were associated with 254 specific diseases and conditions.\u003c/p>\n\u003cp>Concerned about “the public health consequences of inaccurate results,” the FDA asked company founder Anne Wojcicki to stop marketing the health analyses until the “diagnostic and prognostic capability of genomic information has been clinically validated.”\u003c/p>\n\u003cp>23andMe has \u003ca href=\"http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/ucm391016.htm\">stopped marketing\u003c/a> the health analyses in the U.S., but is \u003ca href=\"http://blog.23andme.com/news/update-on-the-regulatory-review-process-with-the-fda/\">working with the FDA\u003c/a> to develop protocols that will allow the company to resume that part of its business.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>23andMe is expected to announce another ten partnerships with pharmaceutical companies over the next several weeks.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/26186/23andme-strikes-another-deal-with-big-pharma","authors":["5432"],"categories":["science_39","science_40"],"tags":["science_304","science_305","science_64","science_458","science_2203"],"featImg":"science_26269","label":"science"},"science_26088":{"type":"posts","id":"science_26088","meta":{"index":"posts_1591205157","site":"science","id":"26088","score":null,"sort":[1421071249000]},"guestAuthors":[],"slug":"scientists-use-modern-dna-to-reconstruct-part-of-a-19th-century-mans-genome","title":"Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome","publishDate":1421071249,"format":"aside","headTitle":"Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_26091\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26091\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\" alt=\"We can now begin to piece back together the DNA of long dead people using the DNA of their modern relatives. (Wikimedia Commons)\" width=\"800\" height=\"532\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We can now begin to piece back together the DNA of individuals from the past using the DNA of their modern relatives. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denslow's_Humpty_Dumpty_pg_5.jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Have you ever wondered about one of your relatives from long ago? Maybe he was famous or you want to know where your family’s blue eyes came from or you’re just plain curious.\u003c/p>\n\u003cp>Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.\u003c/p>\n\u003cp>This is exactly what the good folks at the San Francisco-based company AncestryDNA \u003ca href=\"http://www.foxnews.com/science/2014/12/16/ancestrydna-reconstructs-partial-genome-1th-century-father/\">just did with David Speegle\u003c/a>, a man born sometime around 1806. They were able to use the DNA of Speegle’s living descendants to piece together around 12% of the length of his genome. From this work, they were able to figure out that either he or one of his two wives probably had blue eyes and had the genes for early baldness.\u003c/p>\n\u003cp>This is just a start. As we learn more about human DNA, we will be able to learn a whole lot more about this long dead man from his recreated genome.\u003c/p>\n\u003cp>And now that AncestryDNA has worked out how to do this, they may be able to apply it to other deceased individuals as well. We may soon have a whole new way to learn about our past.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>\u003cstrong>A Little Bit of Luck\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_26093\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26093\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\" alt=\"This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black-and-white photo. (restorationmovement.com)\" width=\"200\" height=\"374\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black and white photo. (\u003ca href=\"http://www.therestorationmovement.com/alabama/speegle.htm\">restorationmovement.com\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone knows that they get half their DNA from their mom and half from their dad. What they might not have thought about is what happens to their DNA if they have just one child. Basically, at its simplest, half their DNA is lost forever!\u003c/p>\n\u003cp>Now of course it isn’t as simple as that. If you have brothers or sisters, they share right around half of their DNA with you and so their kids will share some of your DNA too. And if your parents had brothers and sisters they will share some of your DNA too. And so on.\u003c/p>\n\u003cp>Still, it becomes very tricky to track down DNA from people with few descendants. Which is why David Speegle made such an ideal test case.\u003c/p>\n\u003cp>He had 26(!) kids with two different wives and over 150 grandkids. His full set of DNA was pretty much passed on to the next generation multiple times.\u003c/p>\n\u003cp>This is where the luck comes in. For now, if you wanted something similar done for one of your relatives, you’d need to focus on someone that had lots of kids. That long-lost relative with two kids and four grandkids will probably remain a mystery for the foreseeable future.\u003c/p>\n\u003cp>So the first step is picking a relative with lots of kids and grandkids. But this is by no means the whole story. You also need to know the DNA of lots of your relatives and have lots of accurate, overlapping family trees.\u003c/p>\n\u003cp>\u003cstrong>A Lot of Science and Genealogy\u003c/strong>\u003c/p>\n\u003cp>David Speegle, his kids and his grandkids have all been dead for a very long time. What this means is that anyone alive today has, at most, tiny splinters of his DNA in theirs. These wisps of DNA need to be recognized and then combined to recreate David Speegle’s DNA.\u003c/p>\n\u003cfigure id=\"attachment_26095\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26095\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\" alt=\"We are getting closer to being able to recreate the genomes of long dead people. (Flickr)\" width=\"250\" height=\"375\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting closer to being able to recreate the genomes of long dead people. (\u003ca href=\"https://www.flickr.com/photos/greyloch/9121238998/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Remember, you can’t compare the DNA of a relative with David’s DNA. His DNA is not available.\u003c/p>\n\u003cp>So, basically you are looking at as many of the people as you can at the bottom level of an enormous family tree that starts with David and his two wives. Fortunately, AncestryDNA has a good number of David Speegle’s descendants in the over 500,000 genomes in their database.\u003c/p>\n\u003cp>The researchers at AncestryDNA compared the DNA of all of the pairs of people for whom Speegle was the most recent common ancestor, one pair at a time, and looked for common DNA. They found a whole lot of it.\u003c/p>\n\u003cp>The next step was to find the DNA that is actually David’s and not some other shared relative’s DNA. This is trickier than it sounds because DNA doesn’t get passed down in predictable chunks from generation to generation. It gets all mixed, matched, and diluted in each generation.\u003c/p>\n\u003cp>This is where those family trees come in handy. You can subtract out DNA that is shared because of other relatives.\u003c/p>\n\u003cp>In fact, this is where the David’s two wives really helped. They made it easier to separate out the DNA that came from these two women compared to the DNA that came from David.\u003c/p>\n\u003cp>\u003cstrong>Not Just a Parlor Trick\u003c/strong>\u003c/p>\n\u003cp>Recreating David’s genome is more than just some heroic academic exercise. It also points to what we can learn about ourselves from testing the DNA of many relatives.\u003c/p>\n\u003cp>For example, people are using their DNA to trace their family’s ancestry. In fact, whole companies (including AncestryDNA) are based on just that premise.\u003c/p>\n\u003cp>Unfortunately, you can lose a lot of information if you test only yourself. Remember, you have only half of your mom and dad’s DNA. What this means is that you may miss more distant ancestry information.\u003c/p>\n\u003cp>Imagine that you had an Asian ancestor 5 or 6 generations back. This might mean that your parent has less than 5% of that Asian ancestor’s DNA in his or her DNA. If you happened to not inherit that part of your parent’s DNA, then the history of your Asian ancestry would be lost. (Click \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/uneven-passing-dna\">here \u003c/a>for more information on these scenarios.)\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>One way to recover that information would be through something similar to what was done here for David Speegle. By comparing the DNA of lots of relatives you might be able to piece together that lost Asian history and learn a bit about yourself or confirm a family story.\u003c/p>\n\n","blocks":[],"excerpt":"Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.","status":"publish","parent":0,"modified":1704932415,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":28,"wordCount":1073},"headData":{"title":"Scientists Used Modern DNA to Reconstruct Part of a 19th-Century Man’s Genome | KQED","description":"Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"path":"/science/26088/scientists-use-modern-dna-to-reconstruct-part-of-a-19th-century-mans-genome","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_26091\" class=\"wp-caption aligncenter\" style=\"max-width: 800px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26091\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/HumptyDumpty.jpg\" alt=\"We can now begin to piece back together the DNA of long dead people using the DNA of their modern relatives. (Wikimedia Commons)\" width=\"800\" height=\"532\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We can now begin to piece back together the DNA of individuals from the past using the DNA of their modern relatives. (\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denslow's_Humpty_Dumpty_pg_5.jpg\">Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Have you ever wondered about one of your relatives from long ago? Maybe he was famous or you want to know where your family’s blue eyes came from or you’re just plain curious.\u003c/p>\n\u003cp>Until recently, you pretty much had to rely on family stories that were passed down through the generations to learn about your ancestors. But that is now set to change. With a little luck, a whole lot of science and genealogy, you may be able to use passed down DNA instead of stories to learn a bit about that great-great-great-grandfather.\u003c/p>\n\u003cp>This is exactly what the good folks at the San Francisco-based company AncestryDNA \u003ca href=\"http://www.foxnews.com/science/2014/12/16/ancestrydna-reconstructs-partial-genome-1th-century-father/\">just did with David Speegle\u003c/a>, a man born sometime around 1806. They were able to use the DNA of Speegle’s living descendants to piece together around 12% of the length of his genome. From this work, they were able to figure out that either he or one of his two wives probably had blue eyes and had the genes for early baldness.\u003c/p>\n\u003cp>This is just a start. As we learn more about human DNA, we will be able to learn a whole lot more about this long dead man from his recreated genome.\u003c/p>\n\u003cp>And now that AncestryDNA has worked out how to do this, they may be able to apply it to other deceased individuals as well. We may soon have a whole new way to learn about our past.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>\u003cstrong>A Little Bit of Luck\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_26093\" class=\"wp-caption alignright\" style=\"max-width: 200px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26093\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DSpeegle.jpg\" alt=\"This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black-and-white photo. (restorationmovement.com)\" width=\"200\" height=\"374\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">This is a picture of David Speegle. We can use the DNA of his living relatives to add a bit of color to this black and white photo. (\u003ca href=\"http://www.therestorationmovement.com/alabama/speegle.htm\">restorationmovement.com\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone knows that they get half their DNA from their mom and half from their dad. What they might not have thought about is what happens to their DNA if they have just one child. Basically, at its simplest, half their DNA is lost forever!\u003c/p>\n\u003cp>Now of course it isn’t as simple as that. If you have brothers or sisters, they share right around half of their DNA with you and so their kids will share some of your DNA too. And if your parents had brothers and sisters they will share some of your DNA too. And so on.\u003c/p>\n\u003cp>Still, it becomes very tricky to track down DNA from people with few descendants. Which is why David Speegle made such an ideal test case.\u003c/p>\n\u003cp>He had 26(!) kids with two different wives and over 150 grandkids. His full set of DNA was pretty much passed on to the next generation multiple times.\u003c/p>\n\u003cp>This is where the luck comes in. For now, if you wanted something similar done for one of your relatives, you’d need to focus on someone that had lots of kids. That long-lost relative with two kids and four grandkids will probably remain a mystery for the foreseeable future.\u003c/p>\n\u003cp>So the first step is picking a relative with lots of kids and grandkids. But this is by no means the whole story. You also need to know the DNA of lots of your relatives and have lots of accurate, overlapping family trees.\u003c/p>\n\u003cp>\u003cstrong>A Lot of Science and Genealogy\u003c/strong>\u003c/p>\n\u003cp>David Speegle, his kids and his grandkids have all been dead for a very long time. What this means is that anyone alive today has, at most, tiny splinters of his DNA in theirs. These wisps of DNA need to be recognized and then combined to recreate David Speegle’s DNA.\u003c/p>\n\u003cfigure id=\"attachment_26095\" class=\"wp-caption alignleft\" style=\"max-width: 250px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-26095\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2015/01/DNAbody.jpg\" alt=\"We are getting closer to being able to recreate the genomes of long dead people. (Flickr)\" width=\"250\" height=\"375\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">We are getting closer to being able to recreate the genomes of long dead people. (\u003ca href=\"https://www.flickr.com/photos/greyloch/9121238998/\">Flickr\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Remember, you can’t compare the DNA of a relative with David’s DNA. His DNA is not available.\u003c/p>\n\u003cp>So, basically you are looking at as many of the people as you can at the bottom level of an enormous family tree that starts with David and his two wives. Fortunately, AncestryDNA has a good number of David Speegle’s descendants in the over 500,000 genomes in their database.\u003c/p>\n\u003cp>The researchers at AncestryDNA compared the DNA of all of the pairs of people for whom Speegle was the most recent common ancestor, one pair at a time, and looked for common DNA. They found a whole lot of it.\u003c/p>\n\u003cp>The next step was to find the DNA that is actually David’s and not some other shared relative’s DNA. This is trickier than it sounds because DNA doesn’t get passed down in predictable chunks from generation to generation. It gets all mixed, matched, and diluted in each generation.\u003c/p>\n\u003cp>This is where those family trees come in handy. You can subtract out DNA that is shared because of other relatives.\u003c/p>\n\u003cp>In fact, this is where the David’s two wives really helped. They made it easier to separate out the DNA that came from these two women compared to the DNA that came from David.\u003c/p>\n\u003cp>\u003cstrong>Not Just a Parlor Trick\u003c/strong>\u003c/p>\n\u003cp>Recreating David’s genome is more than just some heroic academic exercise. It also points to what we can learn about ourselves from testing the DNA of many relatives.\u003c/p>\n\u003cp>For example, people are using their DNA to trace their family’s ancestry. In fact, whole companies (including AncestryDNA) are based on just that premise.\u003c/p>\n\u003cp>Unfortunately, you can lose a lot of information if you test only yourself. Remember, you have only half of your mom and dad’s DNA. What this means is that you may miss more distant ancestry information.\u003c/p>\n\u003cp>Imagine that you had an Asian ancestor 5 or 6 generations back. This might mean that your parent has less than 5% of that Asian ancestor’s DNA in his or her DNA. If you happened to not inherit that part of your parent’s DNA, then the history of your Asian ancestry would be lost. (Click \u003ca href=\"http://genetics.thetech.org/ask-a-geneticist/uneven-passing-dna\">here \u003c/a>for more information on these scenarios.)\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>One way to recover that information would be through something similar to what was done here for David Speegle. By comparing the DNA of lots of relatives you might be able to piece together that lost Asian history and learn a bit about yourself or confirm a family story.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/26088/scientists-use-modern-dna-to-reconstruct-part-of-a-19th-century-mans-genome","authors":["6177"],"categories":["science_30"],"tags":["science_305","science_326"],"featImg":"science_26091","label":"science"},"science_17481":{"type":"posts","id":"science_17481","meta":{"index":"posts_1591205157","site":"science","id":"17481","score":null,"sort":[1400508044000]},"guestAuthors":[],"slug":"dna-adding-two-letters-to-lifes-alphabet","title":"DNA 2.0: Adding Two Letters to Life’s Alphabet","publishDate":1400508044,"format":"aside","headTitle":"DNA 2.0: Adding Two Letters to Life’s Alphabet | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_17483\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/StainedGlassDNA.jpg\" rel=\"attachment wp-att-17483\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17483\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/StainedGlassDNA.jpg\" alt=\"The DNA in this stained glass may need two new colors to represent two new bases. (Wikimedia Commons/Schutz)\" width=\"640\" height=\"328\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The DNA in this stained glass may need two new colors to represent two new bases. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Crick-stainedglass-gonville-caius.jpg\">Schutz\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone has heard of the A’s, G’s, C’s, and T’s of DNA. These four letters form the alphabet for the instructions for all life on the planet.\u003c/p>\n\u003cp>Now a group of scientists at Scripps in San Diego have taken the \u003ca href=\"http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13314.html\">first steps to adding two more letters\u003c/a>, d5SICS and dNaM, to this universal genetic code. No catchy single letter code for these unnatural bases yet though. Maybe S and N?\u003c/p>\n\u003cp>The big deal here isn’t that they have found some unnatural new bases they can add to DNA. These have been around for a decade or so. No what makes this astonishing is that a bacterium didn’t mind too much them being there.\u003c/p>\n\u003cp>With a tweak that allowed the bacteria to take up the new bases, the researchers found that the bacteria happily copied the DNA containing these bases and passed them on to the next generation. And they did a pretty good job of it too. Despite a billions of years of optimizing everything for these four letters, the bacteria shrugged off the new ones and just kept going.\u003c/p>\n\u003cp>Well, maybe shrugged off is a bit strong. The bacteria ran into problems if there were too many new letters in a row. But still, the mind boggles at the flexibility of the cellular machinery.\u003c/p>\n\u003cfigure id=\"attachment_17487\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/ET.jpg\" rel=\"attachment wp-att-17487\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17487\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/ET.jpg\" alt=\"A first step towards having six base pairs in our DNA just like E.T. (Wikimedia Commons/Denis Bourez)\" width=\"320\" height=\"240\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A first step towards having six base pairs in our DNA just like E.T. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denis_Bourez_-_Madame_Tussauds,_London_(8747016335).jpg\">Denis Bourez\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>The next step will be to get the cell to read these new letters. Right now, they are copied but not understood. It’s akin to a medieval monk carefully copying Arabic text he doesn’t understand. This will not be easy to teach a cell but it is doable.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>There is \u003ca href=\"http://www.dnalc.org/resources/3d/central-dogma.html\">complicated machinery\u003c/a> in a cell that allows it to read what’s written in DNA. Some of this will have to be redesigned so new words can be added to the cell’s dictionary, but this is a technical not a theoretical hurdle. With enough tinkering, it will get done.\u003c/p>\n\u003cp>So now that we will finally have achieved E.T.’s biology (does anyone else remember he had six bases in his DNA?), the next question is whether this is worth it. Is this the best approach to rejiggering the genetic code? And can these types of changes improve on the current code?\u003c/p>\n\u003cp>\u003cstrong>New Words vs. New Definitions\u003c/strong>\u003c/p>\n\u003cp>All life on Earth uses the same genetic code for its instructions. It’s a very simple language made up of 64 three-letter words made out of a four-letter alphabet. And it isn’t really even that complicated.\u003c/p>\n\u003cp>The 64 words of the language only have around 21 definitions or so. What this means is that a lot of the words have the exact same definition. For example, TAG, TAA, and TGA all mean the same thing.\u003c/p>\n\u003cp>The work here wants to expand the words of the code by adding new letters. All the words will still be three letters long (that is way too hard to change), but now instead of the usual 64 we could have up to 216 words.\u003c/p>\n\u003cfigure id=\"attachment_17489\" class=\"wp-caption alignleft\" style=\"max-width: 275px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/GeneticCode275.jpg\" rel=\"attachment wp-att-17489\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17489\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/GeneticCode275.jpg\" alt=\"Lots of room for making the language of life more complicated. (Wikimedia Commons/NIH)\" width=\"275\" height=\"241\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Lots of room for making the language of life more complicated. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:06_chart_pu3.gif\">NIH\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Of course, since life isn’t getting its full bang for the buck with the 64 words it already has, we may not need such a huge expansion of life’s dictionary. Maybe a better approach is to simply give some of the old words new definitions.\u003c/p>\n\u003cp>As an example, maybe all the TAG’s could be changed into TAA’s and then TAG could be given a new definition. Now we can add something new without changing the alphabet. George Church’s lab is already doing this sort of thing in bacteria and is\u003ca href=\"http://genetics.thetech.org/original_news/news144\"> making real progress\u003c/a>.\u003c/p>\n\u003cp>So it is an open question which is the better approach. If your goal is to genetically engineer some protein with never before seen parts, the new letter approach might be easier. Since life doesn’t already have that word, you don’t need to change it in all of the bacterium’s genes. You would just need to do it in the piece of DNA you are working on.\u003c/p>\n\u003cp>But if you want to make a larger scale change, then it might be better to change the meaning of an old word. With enough changes, this approach gives the added bonus of being resistant to the viruses that use that old, natural genetic code.\u003c/p>\n\u003cp>And of course the new letters aren’t just to form words. They make fundamentally new DNA that can be used by scientists to detect viral infections, make molecules that can better speed up reactions, be used as drugs, and probably lots and lots of other cool things.\u003c/p>\n\u003cp>All of these applications will be incredibly useful but probably aren’t the only driving force behind these experiments. No, the real reasons go much deeper.\u003c/p>\n\u003cp>One of these is undoubtedly a thirst to understand in detail how the current genetic code works. In the process of creating a new language, we will need to completely understand how the old one works.\u003c/p>\n\u003cp>Along the way we may even be able to improve on what Mother Nature has managed to cobble together with billions of years of evolution. After all, while DNA is a marvel, it is far from perfect.\u003c/p>\n\u003cp>\u003cstrong>Good vs. Good Enough\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_17492\" class=\"wp-caption alignright\" style=\"max-width: 257px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNAbasePairs.jpg\" rel=\"attachment wp-att-17492\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17492\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNAbasePairs.jpg\" alt=\"Is this the best you can do Mother Nature? (Wikimedia Commons/Madprime)\" width=\"257\" height=\"299\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Is this the best you can do Mother Nature? (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:DNA_chemical_structure.svg\">Madprime\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>DNA is a great little molecule. It is very stable which is important for storing information for the long haul. And because of its double stranded structure, it is very easily copied and passed on from generation to generation.\u003c/p>\n\u003cp>The key to this last point is base pairing. Every A pairs up with a T and vice versa. The same thing is true for G and C. This arrangement makes it easy to separate the two strands and make a copy by matching up these letters. (This was a key finding from \u003ca href=\"http://en.wikipedia.org/wiki/Molecular_Structure_of_Nucleic_Acids:_A_Structure_for_Deoxyribose_Nucleic_Acid\">Watson and Crick’s original work\u003c/a>.)\u003c/p>\n\u003cp>This is why these researchers had to add two new letters. The S and the N pair up with each other like the G and the C or the A and the T do. But the unnatural bases pair up in a different way.\u003c/p>\n\u003cp>Natural bases use a fairly weak force called hydrogen bonds to line up with one another. Turns out this may not be ideal since water pretty easily disrupts these bonds and cells are filled with water.\u003c/p>\n\u003cp>The new bases use hydrophobic forces which are actually strengthened in the presence of water. This should stabilize the pairing of these bases.\u003c/p>\n\u003cp>Once scientists swap out a lot of a cell’s natural bases for unnatural ones, then maybe we can learn if the weak hydrogen bonds were actually a good idea or if they were the first thing that worked well all those eons ago and life has simply stuck with it. And this won’t be the only thing we might be able to improve upon.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>DNA has a few other properties that at first blush look like they could be improved upon. Scientists may be able to intelligently redesign life so that it has a sturdier and more reliable genetic code. Or it may be that none of our tweaks improves anything much at all. We’ll have to wait and see.\u003c/p>\n\n","blocks":[],"excerpt":"For the last few billion years, all life has used just four letters to spell out its instructions. Now a group in San Diego has added two new letters.","status":"publish","parent":0,"modified":1704933637,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":30,"wordCount":1331},"headData":{"title":"DNA 2.0: Adding Two Letters to Life’s Alphabet | KQED","description":"For the last few billion years, all life has used just four letters to spell out its instructions. Now a group in San Diego has added two new letters.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"path":"/science/17481/dna-adding-two-letters-to-lifes-alphabet","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_17483\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/StainedGlassDNA.jpg\" rel=\"attachment wp-att-17483\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17483\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/StainedGlassDNA.jpg\" alt=\"The DNA in this stained glass may need two new colors to represent two new bases. (Wikimedia Commons/Schutz)\" width=\"640\" height=\"328\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">The DNA in this stained glass may need two new colors to represent two new bases. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Crick-stainedglass-gonville-caius.jpg\">Schutz\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Most everyone has heard of the A’s, G’s, C’s, and T’s of DNA. These four letters form the alphabet for the instructions for all life on the planet.\u003c/p>\n\u003cp>Now a group of scientists at Scripps in San Diego have taken the \u003ca href=\"http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13314.html\">first steps to adding two more letters\u003c/a>, d5SICS and dNaM, to this universal genetic code. No catchy single letter code for these unnatural bases yet though. Maybe S and N?\u003c/p>\n\u003cp>The big deal here isn’t that they have found some unnatural new bases they can add to DNA. These have been around for a decade or so. No what makes this astonishing is that a bacterium didn’t mind too much them being there.\u003c/p>\n\u003cp>With a tweak that allowed the bacteria to take up the new bases, the researchers found that the bacteria happily copied the DNA containing these bases and passed them on to the next generation. And they did a pretty good job of it too. Despite a billions of years of optimizing everything for these four letters, the bacteria shrugged off the new ones and just kept going.\u003c/p>\n\u003cp>Well, maybe shrugged off is a bit strong. The bacteria ran into problems if there were too many new letters in a row. But still, the mind boggles at the flexibility of the cellular machinery.\u003c/p>\n\u003cfigure id=\"attachment_17487\" class=\"wp-caption alignright\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/ET.jpg\" rel=\"attachment wp-att-17487\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17487\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/ET.jpg\" alt=\"A first step towards having six base pairs in our DNA just like E.T. (Wikimedia Commons/Denis Bourez)\" width=\"320\" height=\"240\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">A first step towards having six base pairs in our DNA just like E.T. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:Denis_Bourez_-_Madame_Tussauds,_London_(8747016335).jpg\">Denis Bourez\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>The next step will be to get the cell to read these new letters. Right now, they are copied but not understood. It’s akin to a medieval monk carefully copying Arabic text he doesn’t understand. This will not be easy to teach a cell but it is doable.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>There is \u003ca href=\"http://www.dnalc.org/resources/3d/central-dogma.html\">complicated machinery\u003c/a> in a cell that allows it to read what’s written in DNA. Some of this will have to be redesigned so new words can be added to the cell’s dictionary, but this is a technical not a theoretical hurdle. With enough tinkering, it will get done.\u003c/p>\n\u003cp>So now that we will finally have achieved E.T.’s biology (does anyone else remember he had six bases in his DNA?), the next question is whether this is worth it. Is this the best approach to rejiggering the genetic code? And can these types of changes improve on the current code?\u003c/p>\n\u003cp>\u003cstrong>New Words vs. New Definitions\u003c/strong>\u003c/p>\n\u003cp>All life on Earth uses the same genetic code for its instructions. It’s a very simple language made up of 64 three-letter words made out of a four-letter alphabet. And it isn’t really even that complicated.\u003c/p>\n\u003cp>The 64 words of the language only have around 21 definitions or so. What this means is that a lot of the words have the exact same definition. For example, TAG, TAA, and TGA all mean the same thing.\u003c/p>\n\u003cp>The work here wants to expand the words of the code by adding new letters. All the words will still be three letters long (that is way too hard to change), but now instead of the usual 64 we could have up to 216 words.\u003c/p>\n\u003cfigure id=\"attachment_17489\" class=\"wp-caption alignleft\" style=\"max-width: 275px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/GeneticCode275.jpg\" rel=\"attachment wp-att-17489\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17489\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/GeneticCode275.jpg\" alt=\"Lots of room for making the language of life more complicated. (Wikimedia Commons/NIH)\" width=\"275\" height=\"241\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Lots of room for making the language of life more complicated. (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:06_chart_pu3.gif\">NIH\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Of course, since life isn’t getting its full bang for the buck with the 64 words it already has, we may not need such a huge expansion of life’s dictionary. Maybe a better approach is to simply give some of the old words new definitions.\u003c/p>\n\u003cp>As an example, maybe all the TAG’s could be changed into TAA’s and then TAG could be given a new definition. Now we can add something new without changing the alphabet. George Church’s lab is already doing this sort of thing in bacteria and is\u003ca href=\"http://genetics.thetech.org/original_news/news144\"> making real progress\u003c/a>.\u003c/p>\n\u003cp>So it is an open question which is the better approach. If your goal is to genetically engineer some protein with never before seen parts, the new letter approach might be easier. Since life doesn’t already have that word, you don’t need to change it in all of the bacterium’s genes. You would just need to do it in the piece of DNA you are working on.\u003c/p>\n\u003cp>But if you want to make a larger scale change, then it might be better to change the meaning of an old word. With enough changes, this approach gives the added bonus of being resistant to the viruses that use that old, natural genetic code.\u003c/p>\n\u003cp>And of course the new letters aren’t just to form words. They make fundamentally new DNA that can be used by scientists to detect viral infections, make molecules that can better speed up reactions, be used as drugs, and probably lots and lots of other cool things.\u003c/p>\n\u003cp>All of these applications will be incredibly useful but probably aren’t the only driving force behind these experiments. No, the real reasons go much deeper.\u003c/p>\n\u003cp>One of these is undoubtedly a thirst to understand in detail how the current genetic code works. In the process of creating a new language, we will need to completely understand how the old one works.\u003c/p>\n\u003cp>Along the way we may even be able to improve on what Mother Nature has managed to cobble together with billions of years of evolution. After all, while DNA is a marvel, it is far from perfect.\u003c/p>\n\u003cp>\u003cstrong>Good vs. Good Enough\u003c/strong>\u003c/p>\n\u003cfigure id=\"attachment_17492\" class=\"wp-caption alignright\" style=\"max-width: 257px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNAbasePairs.jpg\" rel=\"attachment wp-att-17492\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17492\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/DNAbasePairs.jpg\" alt=\"Is this the best you can do Mother Nature? (Wikimedia Commons/Madprime)\" width=\"257\" height=\"299\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Is this the best you can do Mother Nature? (Wikimedia Commons/\u003ca class=\"nofancybox\" href=\"http://commons.wikimedia.org/wiki/File:DNA_chemical_structure.svg\">Madprime\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>DNA is a great little molecule. It is very stable which is important for storing information for the long haul. And because of its double stranded structure, it is very easily copied and passed on from generation to generation.\u003c/p>\n\u003cp>The key to this last point is base pairing. Every A pairs up with a T and vice versa. The same thing is true for G and C. This arrangement makes it easy to separate the two strands and make a copy by matching up these letters. (This was a key finding from \u003ca href=\"http://en.wikipedia.org/wiki/Molecular_Structure_of_Nucleic_Acids:_A_Structure_for_Deoxyribose_Nucleic_Acid\">Watson and Crick’s original work\u003c/a>.)\u003c/p>\n\u003cp>This is why these researchers had to add two new letters. The S and the N pair up with each other like the G and the C or the A and the T do. But the unnatural bases pair up in a different way.\u003c/p>\n\u003cp>Natural bases use a fairly weak force called hydrogen bonds to line up with one another. Turns out this may not be ideal since water pretty easily disrupts these bonds and cells are filled with water.\u003c/p>\n\u003cp>The new bases use hydrophobic forces which are actually strengthened in the presence of water. This should stabilize the pairing of these bases.\u003c/p>\n\u003cp>Once scientists swap out a lot of a cell’s natural bases for unnatural ones, then maybe we can learn if the weak hydrogen bonds were actually a good idea or if they were the first thing that worked well all those eons ago and life has simply stuck with it. And this won’t be the only thing we might be able to improve upon.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>DNA has a few other properties that at first blush look like they could be improved upon. Scientists may be able to intelligently redesign life so that it has a sturdier and more reliable genetic code. Or it may be that none of our tweaks improves anything much at all. We’ll have to wait and see.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/17481/dna-adding-two-letters-to-lifes-alphabet","authors":["6177"],"categories":["science_30"],"tags":["science_305","science_791","science_327"],"featImg":"science_17483","label":"science"},"science_17097":{"type":"posts","id":"science_17097","meta":{"index":"posts_1591205157","site":"science","id":"17097","score":null,"sort":[1399298439000]},"guestAuthors":[],"slug":"some-neanderthal-dna-still-evident-in-modern-european-and-asian-populations","title":"Surprising Amount of Neanderthal DNA Still Evident in Modern European and Asian Populations","publishDate":1399298439,"format":"aside","headTitle":"Surprising Amount of Neanderthal DNA Still Evident in Modern European and Asian Populations | KQED","labelTerm":{"site":"science"},"content":"\u003cfigure id=\"attachment_17099\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/NandertalFamily.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/NandertalFamily.jpg\" alt=\"Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (Wikimedia Commons)\" width=\"640\" height=\"360\" class=\"size-full wp-image-17099\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (\u003ca href=\"http://commons.wikimedia.org/wiki/File:Neanderthals_-_Artist's_rendition_of_Earth_approximately_60,000_years_ago.jpg\" class=\"nofancybox\" target=\"_blank\" rel=\"noopener\">NASA/Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Back in 2010, Svante Pääbo’s group from the Max-Planck Institute for Evolutionary Anthropology in Leipzig Germany published the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/20448178\">first big chunk of Neanderthal DNA\u003c/a>. This was a big deal, because it was the first time so much ancient DNA had been sequenced so completely and what they found when they compared this DNA to that of modern humans. It became pretty obvious early on that everyone except Africans shared around 2% of their DNA with Neanderthals.\u003c/p>\n\u003cp>The simplest (although by no means only) explanation for this result is that humans and Neanderthals had babies together before Neanderthals went extinct. Based on this idea, scientists in two separate studies (\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24476670\">here \u003c/a>and \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24476815\">here\u003c/a>) searched the DNA of over 1,000 modern humans to find what Neanderthal DNA still lurks in non-African DNA today.\u003c/p>\n\u003cp>These scientists found that 20-40% of Neanderthal DNA is still hanging out somewhere in these folks’ DNA. That is a whole lot of DNA that’s still around after tens of thousands of years!\u003c/p>\n\u003cp>A close look at this Neanderthal DNA suggested that some of the DNA stayed because it gave the hybrids an advantage. It also suggested that the hybrids had trouble having kids. Neanderthal DNA giveth and it taketh away.\u003c/p>\n\u003cp>\u003cstrong>Better at Surviving in Europe, Worse Fertility\u003c/strong>\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Neanderthals arrived in Europe and Asia hundreds of thousands of years before modern humans did. This gave Neanderthals plenty of time to adapt to the cold and to all of the bacteria, viruses and so on that they had to live with.\u003c/p>\n\u003cfigure id=\"attachment_17103\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/EastFrisia.jpg\" rel=\"attachment wp-att-17103\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17103\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/EastFrisia.jpg\" alt=\"Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there. (Wikimedia Commons/pixelfehler/Matthias Süßen)\" width=\"320\" height=\"236\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there. (Wikimedia Commons/pixelfehler/\u003ca href=\"http://commons.wikimedia.org/wiki/File:Nebelostfriesland.jpg\" class=\"nofancybox\">Matthias Süßen\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>When modern humans ventured out of Africa all those years later, they were undoubtedly assaulted by a range of bacteria and viruses they had never seen before (think \u003ca href=\"http://www.pbs.org/gunsgermssteel/variables/smallpox.html\">smallpox in the New World\u003c/a>). One way to survive the onslaught would be to have kids with the locals who had already adapted. Sure, you might still have problems, but your kids would definitely do better.\u003c/p>\n\u003cp>When you look at the Neanderthal DNA that has survived, you see \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/21868630\">a whole lot of immune genes\u003c/a>. (The same is true for another ancestor, the \u003ca href=\"http://science.kqed.org/quest/2011/01/17/meet-our-newest-relative/\">Denisovans\u003c/a>.) This strongly suggests that interbreeding gave the hybrids the immune genes they needed to survive in this new environment.\u003c/p>\n\u003cp>You also see a lot of genes that have to do with skin and hair (keratinocyte genes). Although not yet proven, one idea is that some modern humans still have these because they helped them deal with the cold of the northern parts of Asia and Europe.\u003c/p>\n\u003cp>There has also been a\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24336922\"> recent study\u003c/a> that suggests that a bit of Neanderthal DNA that helps deal with ultraviolet light is very common in East Asians. This makes sense given the lighter skin needed to \u003ca href=\"http://genetics.thetech.org/ask/ask330\">get vitamin D up north\u003c/a>. And scientists keep finding more genes like this (click \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24690587\">here \u003c/a>for one dealing with fat metabolism in Europeans).\u003c/p>\n\u003caside class=\"pullquote alignleft\">Neanderthal DNA giveth and it taketh away\u003c/aside>\n\u003cp>Of course nothing in life is free. If you are going to breed with Neanderthals, you are probably going to have some problems too.\u003c/p>\n\u003cp>When you look for Neanderthal DNA in human DNA, you quickly realize that there is hardly any of it on the chromosomes that determine gender, the X and the Y. When this sort of thing is seen in the lab with fruit flies, it comes from something called hybrid sterility. Basically while humans and Neanderthals weren’t quite horses and donkeys, they were close. In other words, the hybrid kids weren’t sterile but they may have had trouble having kids themselves.\u003c/p>\n\u003cp>Taken together these results suggest that the interbreeding of humans and Neanderthals gave enough useful traits to overcome the lowered fertility. Of course this assumes that Neanderthals and humans did have kids together.\u003c/p>\n\u003cp>\u003cstrong>Ancient vs. “Recent” Mingling\u003c/strong>\u003c/p>\n\u003cp>The results showing Neanderthal DNA in some modern human DNA does not necessarily mean the two had kids together when modern humans left Africa. Another less likely but plausible possibility is that the similarity between non-Africans and Neanderthals has to do with them having common ancestors a bit different from those of modern Africans. Both have human ancestors they just come from different gene pools.\u003c/p>\n\u003cfigure id=\"attachment_17107\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Africa.jpg\" rel=\"attachment wp-att-17107\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17107\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Africa.jpg\" alt=\"Scientists may soon be able to pull ancient DNA out of modern Africans' DNA without any fossils. (Wikimedia Commons)\" width=\"300\" height=\"316\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Scientists may soon be able to pull ancient DNA out of modern Africans’ DNA without any fossils. (\u003ca href=\"http://commons.wikimedia.org/wiki/File:Africa_satellite_plane.jpg\" class=\"nofancybox\">NASA/Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>In a simplified version, imagine that a few hundred thousand years ago or so our ancestors in Africa split into two groups. One group stayed in Southern Africa and one left to go north. Some of northern folks went on to Europe and Asia and some stayed behind.\u003c/p>\n\u003cp>The group that left Africa went on to become Neanderthals while both groups in Africa went on to become humans (there was obviously some mingling between the African groups). Then a group of humans from the northern group leaves Africa to settle Europe and Asia. Once they got there, these folks wiped out the Neanderthals that had left their group a few hundred thousand years before.\u003c/p>\n\u003cp>In this scenario, European and Asian DNA would share more in common with Neanderthal DNA than they would with African DNA. The Neanderthals and the Europeans/Asians all started from the same pool of DNA.\u003c/p>\n\u003cp>As I said, this scenario is much less likely. And now a \u003ca href=\"http://www.genetics.org/content/196/4/1241\">new study\u003c/a> shows that it probably didn’t happen this way as humans and Neanderthals almost certainly had kids together.\u003c/p>\n\u003cp>By comparing small bits of the DNA of a human, a Neanderthal and a third ancestor, a Denisovan, these authors provide strong evidence that all three are related because of interbreeding. In the absence of stumbling on a fossil from one of the original hybrids, this is about as strong of evidence as we are going to get for interbreeding.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>Our randy ancestors bred with whomever they came across to birth hybrids that went on to become Europeans and Asians. And the same is probably true for Africans although their interbreeding would have been with other nearby relatives instead of Neanderthals. One day soon we may be able to pull those ancestors’ DNA out of modern African DNA the way we did with Neanderthal DNA in European and Asian DNA. This method is critical for this as we probably won’t get much useable DNA from fossils in tropical areas.\u003c/p>\n\n","blocks":[],"excerpt":"Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern Europeans and Asians because of interbreeding. Neanderthal DNA survives because it gave useful traits to the ancestors of Europeans and Asians.","status":"publish","parent":0,"modified":1704933730,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":23,"wordCount":1120},"headData":{"title":"Surprising Amount of Neanderthal DNA Still Evident in Modern European and Asian Populations | KQED","description":"Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern Europeans and Asians because of interbreeding. Neanderthal DNA survives because it gave useful traits to the ancestors of Europeans and Asians.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":""},"sticky":false,"path":"/science/17097/some-neanderthal-dna-still-evident-in-modern-european-and-asian-populations","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_17099\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/NandertalFamily.jpg\">\u003cimg loading=\"lazy\" decoding=\"async\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/NandertalFamily.jpg\" alt=\"Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (Wikimedia Commons)\" width=\"640\" height=\"360\" class=\"size-full wp-image-17099\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Neanderthals may be extinct but at least 20-40% of their DNA lives on in modern humans. (\u003ca href=\"http://commons.wikimedia.org/wiki/File:Neanderthals_-_Artist's_rendition_of_Earth_approximately_60,000_years_ago.jpg\" class=\"nofancybox\" target=\"_blank\" rel=\"noopener\">NASA/Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>Back in 2010, Svante Pääbo’s group from the Max-Planck Institute for Evolutionary Anthropology in Leipzig Germany published the \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/20448178\">first big chunk of Neanderthal DNA\u003c/a>. This was a big deal, because it was the first time so much ancient DNA had been sequenced so completely and what they found when they compared this DNA to that of modern humans. It became pretty obvious early on that everyone except Africans shared around 2% of their DNA with Neanderthals.\u003c/p>\n\u003cp>The simplest (although by no means only) explanation for this result is that humans and Neanderthals had babies together before Neanderthals went extinct. Based on this idea, scientists in two separate studies (\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24476670\">here \u003c/a>and \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24476815\">here\u003c/a>) searched the DNA of over 1,000 modern humans to find what Neanderthal DNA still lurks in non-African DNA today.\u003c/p>\n\u003cp>These scientists found that 20-40% of Neanderthal DNA is still hanging out somewhere in these folks’ DNA. That is a whole lot of DNA that’s still around after tens of thousands of years!\u003c/p>\n\u003cp>A close look at this Neanderthal DNA suggested that some of the DNA stayed because it gave the hybrids an advantage. It also suggested that the hybrids had trouble having kids. Neanderthal DNA giveth and it taketh away.\u003c/p>\n\u003cp>\u003cstrong>Better at Surviving in Europe, Worse Fertility\u003c/strong>\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Neanderthals arrived in Europe and Asia hundreds of thousands of years before modern humans did. This gave Neanderthals plenty of time to adapt to the cold and to all of the bacteria, viruses and so on that they had to live with.\u003c/p>\n\u003cfigure id=\"attachment_17103\" class=\"wp-caption alignleft\" style=\"max-width: 320px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/EastFrisia.jpg\" rel=\"attachment wp-att-17103\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17103\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/EastFrisia.jpg\" alt=\"Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there. (Wikimedia Commons/pixelfehler/Matthias Süßen)\" width=\"320\" height=\"236\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Neanderthals had time to adapt to chilly northern Europe and Asia and kindly contributed genes to help humans survive when they moved there. (Wikimedia Commons/pixelfehler/\u003ca href=\"http://commons.wikimedia.org/wiki/File:Nebelostfriesland.jpg\" class=\"nofancybox\">Matthias Süßen\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>When modern humans ventured out of Africa all those years later, they were undoubtedly assaulted by a range of bacteria and viruses they had never seen before (think \u003ca href=\"http://www.pbs.org/gunsgermssteel/variables/smallpox.html\">smallpox in the New World\u003c/a>). One way to survive the onslaught would be to have kids with the locals who had already adapted. Sure, you might still have problems, but your kids would definitely do better.\u003c/p>\n\u003cp>When you look at the Neanderthal DNA that has survived, you see \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/21868630\">a whole lot of immune genes\u003c/a>. (The same is true for another ancestor, the \u003ca href=\"http://science.kqed.org/quest/2011/01/17/meet-our-newest-relative/\">Denisovans\u003c/a>.) This strongly suggests that interbreeding gave the hybrids the immune genes they needed to survive in this new environment.\u003c/p>\n\u003cp>You also see a lot of genes that have to do with skin and hair (keratinocyte genes). Although not yet proven, one idea is that some modern humans still have these because they helped them deal with the cold of the northern parts of Asia and Europe.\u003c/p>\n\u003cp>There has also been a\u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24336922\"> recent study\u003c/a> that suggests that a bit of Neanderthal DNA that helps deal with ultraviolet light is very common in East Asians. This makes sense given the lighter skin needed to \u003ca href=\"http://genetics.thetech.org/ask/ask330\">get vitamin D up north\u003c/a>. And scientists keep finding more genes like this (click \u003ca href=\"http://www.ncbi.nlm.nih.gov/pubmed/24690587\">here \u003c/a>for one dealing with fat metabolism in Europeans).\u003c/p>\n\u003caside class=\"pullquote alignleft\">Neanderthal DNA giveth and it taketh away\u003c/aside>\n\u003cp>Of course nothing in life is free. If you are going to breed with Neanderthals, you are probably going to have some problems too.\u003c/p>\n\u003cp>When you look for Neanderthal DNA in human DNA, you quickly realize that there is hardly any of it on the chromosomes that determine gender, the X and the Y. When this sort of thing is seen in the lab with fruit flies, it comes from something called hybrid sterility. Basically while humans and Neanderthals weren’t quite horses and donkeys, they were close. In other words, the hybrid kids weren’t sterile but they may have had trouble having kids themselves.\u003c/p>\n\u003cp>Taken together these results suggest that the interbreeding of humans and Neanderthals gave enough useful traits to overcome the lowered fertility. Of course this assumes that Neanderthals and humans did have kids together.\u003c/p>\n\u003cp>\u003cstrong>Ancient vs. “Recent” Mingling\u003c/strong>\u003c/p>\n\u003cp>The results showing Neanderthal DNA in some modern human DNA does not necessarily mean the two had kids together when modern humans left Africa. Another less likely but plausible possibility is that the similarity between non-Africans and Neanderthals has to do with them having common ancestors a bit different from those of modern Africans. Both have human ancestors they just come from different gene pools.\u003c/p>\n\u003cfigure id=\"attachment_17107\" class=\"wp-caption alignleft\" style=\"max-width: 300px\">\u003ca href=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Africa.jpg\" rel=\"attachment wp-att-17107\">\u003cimg loading=\"lazy\" decoding=\"async\" class=\"size-full wp-image-17107\" src=\"http://ww2.kqed.org/science/wp-content/uploads/sites/35/2014/05/Africa.jpg\" alt=\"Scientists may soon be able to pull ancient DNA out of modern Africans' DNA without any fossils. (Wikimedia Commons)\" width=\"300\" height=\"316\">\u003c/a>\u003cfigcaption class=\"wp-caption-text\">Scientists may soon be able to pull ancient DNA out of modern Africans’ DNA without any fossils. (\u003ca href=\"http://commons.wikimedia.org/wiki/File:Africa_satellite_plane.jpg\" class=\"nofancybox\">NASA/Wikimedia Commons\u003c/a>)\u003c/figcaption>\u003c/figure>\n\u003cp>In a simplified version, imagine that a few hundred thousand years ago or so our ancestors in Africa split into two groups. One group stayed in Southern Africa and one left to go north. Some of northern folks went on to Europe and Asia and some stayed behind.\u003c/p>\n\u003cp>The group that left Africa went on to become Neanderthals while both groups in Africa went on to become humans (there was obviously some mingling between the African groups). Then a group of humans from the northern group leaves Africa to settle Europe and Asia. Once they got there, these folks wiped out the Neanderthals that had left their group a few hundred thousand years before.\u003c/p>\n\u003cp>In this scenario, European and Asian DNA would share more in common with Neanderthal DNA than they would with African DNA. The Neanderthals and the Europeans/Asians all started from the same pool of DNA.\u003c/p>\n\u003cp>As I said, this scenario is much less likely. And now a \u003ca href=\"http://www.genetics.org/content/196/4/1241\">new study\u003c/a> shows that it probably didn’t happen this way as humans and Neanderthals almost certainly had kids together.\u003c/p>\n\u003cp>By comparing small bits of the DNA of a human, a Neanderthal and a third ancestor, a Denisovan, these authors provide strong evidence that all three are related because of interbreeding. In the absence of stumbling on a fossil from one of the original hybrids, this is about as strong of evidence as we are going to get for interbreeding.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Our randy ancestors bred with whomever they came across to birth hybrids that went on to become Europeans and Asians. And the same is probably true for Africans although their interbreeding would have been with other nearby relatives instead of Neanderthals. One day soon we may be able to pull those ancestors’ DNA out of modern African DNA the way we did with Neanderthal DNA in European and Asian DNA. This method is critical for this as we probably won’t get much useable DNA from fossils in tropical areas.\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/science/17097/some-neanderthal-dna-still-evident-in-modern-european-and-asian-populations","authors":["6177"],"categories":["science_30"],"tags":["science_305","science_327"],"featImg":"science_17099","label":"science"}},"programsReducer":{"possible":{"id":"possible","title":"Possible","info":"Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. Together in Possible, Hoffman and Finger lead enlightening discussions about building a brighter collective future. The show features interviews with visionary guests like Trevor Noah, Sam Altman and Janette Sadik-Khan. Possible paints an optimistic portrait of the world we can create through science, policy, business, art and our shared humanity. It asks: What if everything goes right for once? How can we get there? Each episode also includes a short fiction story generated by advanced AI GPT-4, serving as a thought-provoking springboard to speculate how humanity could leverage technology for good.","airtime":"SUN 2pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Possible-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.possible.fm/","meta":{"site":"news","source":"Possible"},"link":"/radio/program/possible","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/possible/id1677184070","spotify":"https://open.spotify.com/show/730YpdUSNlMyPQwNnyjp4k"}},"1a":{"id":"1a","title":"1A","info":"1A is home to the national conversation. 1A brings on great guests and frames the best debate in ways that make you think, share and engage.","airtime":"MON-THU 11pm-12am","imageSrc":"https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/04/1a.jpg","officialWebsiteLink":"https://the1a.org/","meta":{"site":"news","source":"npr"},"link":"/radio/program/1a","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=1188724250&at=11l79Y&ct=nprdirectory","tuneIn":"https://tunein.com/radio/1A-p947376/","rss":"https://feeds.npr.org/510316/podcast.xml"}},"all-things-considered":{"id":"all-things-considered","title":"All Things Considered","info":"Every weekday, \u003cem>All Things Considered\u003c/em> hosts Robert Siegel, Audie Cornish, Ari Shapiro, and Kelly McEvers present the program's trademark mix of news, interviews, commentaries, reviews, and offbeat features. 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But is this once sleepy suburb ready for them?","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/American-Suburb-Podcast-Tile-703x703-1.jpg","officialWebsiteLink":"/news/series/american-suburb-podcast","meta":{"site":"news","source":"kqed","order":"13"},"link":"/news/series/american-suburb-podcast/","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?mt=2&id=1287748328","tuneIn":"https://tunein.com/radio/American-Suburb-p1086805/","rss":"https://ww2.kqed.org/news/series/american-suburb-podcast/feed/podcast","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkMzMDExODgxNjA5"}},"baycurious":{"id":"baycurious","title":"Bay Curious","tagline":"Exploring the Bay Area, one question at a time","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","imageAlt":"\"KQED Bay Curious","officialWebsiteLink":"/news/series/baycurious","meta":{"site":"news","source":"kqed","order":"4"},"link":"/podcasts/baycurious","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/bay-curious/id1172473406","npr":"https://www.npr.org/podcasts/500557090/bay-curious","rss":"https://ww2.kqed.org/news/category/bay-curious-podcast/feed/podcast","google":"https://podcasts.google.com/feed/aHR0cHM6Ly93dzIua3FlZC5vcmcvbmV3cy9jYXRlZ29yeS9iYXktY3VyaW91cy1wb2RjYXN0L2ZlZWQvcG9kY2FzdA","stitcher":"https://www.stitcher.com/podcast/kqed/bay-curious","spotify":"https://open.spotify.com/show/6O76IdmhixfijmhTZLIJ8k"}},"bbc-world-service":{"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":{"site":"news","source":"BBC World Service"},"link":"/radio/program/bbc-world-service","subscribe":{"apple":"https://itunes.apple.com/us/podcast/global-news-podcast/id135067274?mt=2","tuneIn":"https://tunein.com/radio/BBC-World-Service-p455581/","rss":"https://podcasts.files.bbci.co.uk/p02nq0gn.rss"}},"code-switch-life-kit":{"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 />","airtime":"SUN 9pm-10pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Code-Switch-Life-Kit-Podcast-Tile-360x360-1.jpg","meta":{"site":"radio","source":"npr"},"link":"/radio/program/code-switch-life-kit","subscribe":{"apple":"https://podcasts.apple.com/podcast/1112190608?mt=2&at=11l79Y&ct=nprdirectory","google":"https://podcasts.google.com/feed/aHR0cHM6Ly93d3cubnByLm9yZy9yc3MvcG9kY2FzdC5waHA_aWQ9NTEwMzEy","spotify":"https://open.spotify.com/show/3bExJ9JQpkwNhoHvaIIuyV","rss":"https://feeds.npr.org/510312/podcast.xml"}},"commonwealth-club":{"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. 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