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1000 GENOMES PROJECT

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  • manth43470@...
    Perhaps some of you have seen the front page article in today s (18 January 2013) New York Times, Search of DNA Sequences Reveals Full Identities. Data are
    Message 1 of 6 , Jan 18, 2013
      Perhaps some of you have seen the front page article in today's (18 January 2013) New York Times, "Search of DNA Sequences Reveals Full Identities."  Data are from 1000 Genomes Project.  It is not too surprising but a little unnerving, nevertheless.
       
      Mike Anthony
      Kit #18187
      I-M223, CTS6433* (Cont2a)
      U5a1b1a (Grp3)
      Orcadian 100% +/- 0.01 %
    • Dora Smith
      Here’s the url. NYT wants to make a profit and sell access to their site above all things, so getting to the article isn’t that easy.
      Message 2 of 6 , Jan 18, 2013
        Here’s the url.   NYT wants to make a profit and sell access to their site above all things, so getting to the article isn’t that easy.  
         
        I tried hard to identify three participants in the thousand genomes study who have a rare haplogroup I1 SNP, in order to contact them and get more information on their background, and I couldn’t do it.  It is true that only their data and country of origin is provided, and you have to go around Robin Hood’s Barn to get to the data.  
         
        I notice that the article never specifies just HOW they were able to get any information at all.  That means they don’t present any evidence that they are telling the truth.   Never mind who the people they identified were; they don’t provide any evidence they are telling the truth at all.  
         
        I think this is the New York Times trying to get people to buy online subscriptions.  Someone with more clout than me needs to call them on it.   IF they got all this information, HOW specifically was it possible.   If I were the Thousand Genomes Project, I’d sue for libel based on what’s in that article.   If they were able to get that information, then the Thousand Genomes Project has failed to protect their private data.   So if they DID get it, they have to prove how they were able to do it.   That article doesn’t even convince me it was possible.   These are responsible research scientists, not the owners/ principal investors of Google!
         
        Confidential information is kept on all research subjects, even those who participate in those large sociological surveys; not just genetic data.   They have to safeguard the data.   Barring actual evidence to the contrary, I’m sure they did.   If that information were not rseponsibly protected, it would not be possible for scientists to conduct research.   Not surveys, not drug studies, not cancer studies, not diabetes studies, not heart disease studies, not surveys of who you’re going to vote for, not NOTHING.
         
        What’s more, as long as the researchers removed identifying information from the data itself, if someone got into the other place where they kept the confidential data, then either the New York Times reporter committed a criminal act, or the people maintaining the data made some very serious slip in security, and probably both.  
         
        As far as being able to find peoples’ entire families once you know who they are, that’s a piece of cake and has been for some time.   It’s in your credit report, and nobody has to even request a $15 basic background check to learn the names of family members.   Try and look up anybody’s phone number at anywho.com or whitepages.com .
         
        Several years ago my mother in law wanted to see what I could learn about her biological mother.   All she had was the woman’s name, the names of the aunts who raised her and the place where they lived.   One specific question was what happened to the woman.  I was able to learn what happened to her, what she died of, who she married, who was her daughter, who the daughter married, and the names, locations and occupations of both her children, without a whole lot of effort.   I did splurge on the $15 thing. 
         
        A couple of years ago a piece of e-mail I got caused me to think my checking account had been compromised.  I think we ended up issuing me a new card but leaving the checking account as was.   Bank officer assured me that all the info they provided me, including my social security number and my date of birth, is public information.  
         
        Dora
         
        Sent: Friday, January 18, 2013 10:20 AM
        Subject: [I-M223] 1000 GENOMES PROJECT
         
         

        Perhaps some of you have seen the front page article in today's (18 January 2013) New York Times, "Search of DNA Sequences Reveals Full Identities."  Data are from 1000 Genomes Project.  It is not too surprising but a little unnerving, nevertheless.
         
        Mike Anthony
        Kit #18187
        I-M223, CTS6433* (Cont2a)
        U5a1b1a (Grp3)
        Orcadian 100% +/- 0.01 %
      • Dora Smith
        Actually, it DOES eventually say how they were able to identify some research subjects. They matched the data to genetic Y DNA data that is freely available
        Message 3 of 6 , Jan 18, 2013
          Actually, it DOES eventually say how they were able to identify some research subjects.  They matched the data to genetic Y DNA data that is freely available online and identifies the people, because the people themselves submitted it.     Then they went fishing for who with that Y DNA actually was the research subject.   In several cases that wasn’t hard because the people had unusual names and lived in confined areas such as “Utah”.   But if everyone they contacted had said no, that wasn’t me, they’d not have known who it was!   But they would have known who all the cousins were if they wanted to.   You can research anyone’s genealogy.  So can I.  
           
          Moreover, if I’m interested enough to search some Jo Schmo’s genealogy, most often someone else was interested in it before me.   I don’t randomely get that interested; there is for example the new junior Senator from Massachusetts, Elizabeth Warren.  She looks New ENgland, possibly distantly related to me.   Well, she’s neither from New England or distantly related to me.    She did claim for the benefit of whatever for years to be part American Indian.    A lot of people picked up on that, including a first cousin, who has the entire family tree online.   I found the story dismantled in some detail several times online.    And guess what.  She’s not got a drop of American Indian blood – unless her grandmother’s father wasn’t the man who was married to her mother.   The father SHOT an Indian.  Not WAS an Indian.       Whole family were consistently identified as White.  We’ve heard that before.   But she’ll have to do more than that if she wants to claim to be part Indian.   She was making this claim to meet diversity requirements at the universities where she taught, and at those Harvard faculty teas to make conversation.   What is more, if say a great grandparent WAS an Indian.    If noone since that person ever claimed to be an Indian, and noone belonged to a Tribe, that doesn’t qualify her to a claim of being Indian for the purposes of genetic diversity.   You have to see the woman – blond, fair skinned, and looks like a Noyes or a Balch, or half the other women of Massachusetts.   None of her ancestry can be traced back very far, because none of her ancestors actually cared who they were, which leaves one wondering how she’d have any moral character.   I learned from census data that her paternal grandfather was one of the lower middle class people she’s made a career out of purporting to want to help, but she’s never said a word about that.  
           
          But they couldn’t identify the individual project recipient from that unless they had an unusual name or lived in a small place, like one of the people I was trying to find, AND a male line relative made the Y DNA haplotype public.   One of the names was Ventner; that qualifies.   Many of the project participants were in Utah, and which ones those were was identified.    They didn’t have to live in Utah, but that was a good bet for anyone trying to find them.  I know this because one of the three people I wanted to identify lives in Utah.   Or, rather, was in the “Utah” sample.   I would have had to get the data, which I didn’t get to, and figure out how to reconstruct the STR’s from that raw data, which is why I didn’t bother getting the data, to match it up with what is in the public databases.   I thought that would be hard at my level of expertise, and I’m not stupid.   It would take a knowledgeable person and not the hacker down the street.  
           
          The chances aren’t all that low that the people themselves had made their own Y DNA data public.  One would expect people who would volunteer for such a project to be far more knowledgeable than average and active in a number of things along the same lines.  
           
          So, the New York Times headline is completely misleading.
           
          Dora
           
          Sent: Friday, January 18, 2013 12:25 PM
          Subject: Re: [I-M223] 1000 GENOMES PROJECT
           
           

          Here’s the url.   NYT wants to make a profit and sell access to their site above all things, so getting to the article isn’t that easy.  
           
          I tried hard to identify three participants in the thousand genomes study who have a rare haplogroup I1 SNP, in order to contact them and get more information on their background, and I couldn’t do it.  It is true that only their data and country of origin is provided, and you have to go around Robin Hood’s Barn to get to the data.  
           
          I notice that the article never specifies just HOW they were able to get any information at all.  That means they don’t present any evidence that they are telling the truth.   Never mind who the people they identified were; they don’t provide any evidence they are telling the truth at all.  
           
          I think this is the New York Times trying to get people to buy online subscriptions.  Someone with more clout than me needs to call them on it.   IF they got all this information, HOW specifically was it possible.   If I were the Thousand Genomes Project, I’d sue for libel based on what’s in that article.   If they were able to get that information, then the Thousand Genomes Project has failed to protect their private data.   So if they DID get it, they have to prove how they were able to do it.   That article doesn’t even convince me it was possible.   These are responsible research scientists, not the owners/ principal investors of Google!
           
          Confidential information is kept on all research subjects, even those who participate in those large sociological surveys; not just genetic data.   They have to safeguard the data.   Barring actual evidence to the contrary, I’m sure they did.   If that information were not rseponsibly protected, it would not be possible for scientists to conduct research.   Not surveys, not drug studies, not cancer studies, not diabetes studies, not heart disease studies, not surveys of who you’re going to vote for, not NOTHING.
           
          What’s more, as long as the researchers removed identifying information from the data itself, if someone got into the other place where they kept the confidential data, then either the New York Times reporter committed a criminal act, or the people maintaining the data made some very serious slip in security, and probably both.  
           
          As far as being able to find peoples’ entire families once you know who they are, that’s a piece of cake and has been for some time.   It’s in your credit report, and nobody has to even request a $15 basic background check to learn the names of family members.   Try and look up anybody’s phone number at anywho.com or whitepages.com .
           
          Several years ago my mother in law wanted to see what I could learn about her biological mother.   All she had was the woman’s name, the names of the aunts who raised her and the place where they lived.   One specific question was what happened to the woman.  I was able to learn what happened to her, what she died of, who she married, who was her daughter, who the daughter married, and the names, locations and occupations of both her children, without a whole lot of effort.   I did splurge on the $15 thing. 
           
          A couple of years ago a piece of e-mail I got caused me to think my checking account had been compromised.  I think we ended up issuing me a new card but leaving the checking account as was.   Bank officer assured me that all the info they provided me, including my social security number and my date of birth, is public information.  
           
          Dora
           
          Sent: Friday, January 18, 2013 10:20 AM
          Subject: [I-M223] 1000 GENOMES PROJECT
           
           

          Perhaps some of you have seen the front page article in today's (18 January 2013) New York Times, "Search of DNA Sequences Reveals Full Identities."  Data are from 1000 Genomes Project.  It is not too surprising but a little unnerving, nevertheless.
           
          Mike Anthony
          Kit #18187
          I-M223, CTS6433* (Cont2a)
          U5a1b1a (Grp3)
          Orcadian 100% +/- 0.01 %
        • John S. Quarterman
          A poster wandered far off topic to repeat gossip about Sen. Elizabeth Warren. Let s use that as a learning opportunity. Here s Warren s own statement:
          Message 4 of 6 , Jan 18, 2013
            A poster wandered far off topic to repeat gossip about Sen. Elizabeth
            Warren. Let's use that as a learning opportunity.

            Here's Warren's own statement:

            http://www.boston.com/news/politics/2012/senate/specials/elizabeth_warren_statement/

            This claim, "She was making this claim to meet diversity requirements
            at the universities where she taught...." is simply not true:

            http://www.washingtonpost.com/blogs/fact-checker/post/everything-you-need-to-know-about-the-controversy-over-elizabeth-warrens-claimed-native-american-heritage/2012/09/27/d0b7f568-08a5-11e2-a10c-fa5a255a9258_blog.html

            Back to Warren's ancestry. Here's a writeup about that:

            http://www.pollysgranddaughter.com/2012/09/elizabeth-warrens-reed-and-crawford.html

            It includes things like this:

            "Both the Reeds and Crawfords are ALWAYS found on federal census forms as
            white, going back as far as they can be traced on the federal census. They
            are white in EVERY other record they are found on as well. They are also
            found in NO Cherokee records, ever. Because the Delaware were adopted by
            the Cherokee Nation, from that time forward, they should be found in the
            Cherokee historical records if they were truly Cherokee or Delaware. They
            are not."

            Does that mean Warren was lying? No, it means she isn't a genealogist,
            and she believed what her relatives told her.

            "Both families are documented as white in all historical documents. Are
            we supposed to believe that there huge conspiracies in both families
            to cover up Indian blood and record themselves as white for as long as
            records have been kept in the United States? Or is it more likely someone
            along the way either got confused or made up stories about each of the
            families and now some descendants accept the stories as true?"

            Exactly.

            My grandmother was more curious, and turned into a genealogist
            because of it. Some people said her family was of Indian ancestry.
            Turns out we're descended from the *brother* of Creek Indian Chief
            William McIntosh. In this case, it was other people who said
            we were Indian, not family, but it was still a case of mythology
            being believed.

            And how about Henry Louis Gates, who was told by one DNA company
            that "his maternal ancestry could most likely be traced back to
            Egypt, probably to the Nubian ethnic group. Five years later,
            however, a test by a second company startled him. It concluded
            that his maternal ancestors were not Nubian or even African,
            but most likely European."

            Should he be slandered up and down the town for believing what a
            purportedly scientific company told him?

            On the other hand, I could list quite a few family stories from my
            family and allied families that turn out to be quite true, backed
            up now by genealogical research and in some cases by DNA.

            So, how about we give anybody who believes old family stories the
            benefit of the doubt, even if the stories turn out not to be true?

            -jsq
          • Dora Smith
            Not true, huh? Hmmm. Well, since it’s off topic, I’ll leave it alone. I already don’t think too much of the woman, and if she double proved she’s
            Message 5 of 6 , Jan 18, 2013
              Not true, huh?    Hmmm.  Well, since it’s off topic, I’ll leave it alone.  I already don’t think too much of the woman, and if she double proved she’s a liar, I don’t feel like dealing with it at the moment.
               
              No, wait.  I actually know for a fact she claimed it.   She provided all of the information on the subject of her grandmother being part Indian, to a cousin who has the family history online.  Cousin individually cited her as the source for each detail of the story she told her.   The cousin is one of several people who tore the story apart.  I looked into it too, and certainly every single person involved and all of their immediate forebears were identified at the time as White.  So if she’s saying she didn’t say it, she’s lying.  And enough people have claimed to have heard her say it, plus she apparently made the claim in writing on her applications to two universities where she taught.   AND, I myself saw her own personal direct statement that the story is the truth.   Well, so much for Elizabeth Warren.   I’m actively avoiding seeing Lance Armstrong’s face, and I guess she’s just going to have to get on the list.  Maybe next week, if I remember she exists, I’ll pursue those links and let her have it, since I can certainly prove she really said it.   If now she’s really saying she didn’t say it.   She could always be trying to pretend it doesn’t matter instead.   Now, don’t get me started, or I’ll say something about the OTHER Senator from Massachusetts.   Honest, I’m a liberal Democrat, but it’s no astonishment to me they keep losing elections.  
               
              One thing, though.   Back on topic.   Vicious grin.    The original post directed us to a New York Times article.   The New York Times article is not the original article, as hard as it is to believe.   The original articles – three of them, hoping that if they pound it in three times it’ll take better, or something, are in the current issue of Science.  They’ve been made available online, due to the overwhelming urgency of getting us to drop genetic genealogy immediately.
               
              I read every detail, carefully, except the part about who wrote it.   It is natural to believe a reporter would do something like that rather than scientists – genetic scientists and experts on genetic diseases of particular ethnic groups, no less.   It’s outrageous enough if a reporter had done it – but in character.   Pay close attention to the details of what they did, now.   They THOUGHT they identified a match to some Thousand Genomes data in public STR marker databases, and then they got on the phone, and called people up, all over Utah, and asked them if it was them.    In one case they worked backwards, since they already knew whose data it was, and he has an unusual name.  
               
              Still choking.  But I have to rewrite my comment.   I wrongly blamed some hoity-toity New York Times reporter.   Shot the messenger, in other words.   Reporter was considerably tamer than the New Scientist article about it!   Urgh!   Honestly!   
               
              Yours,
              Dora Smith
               
              Sent: Friday, January 18, 2013 8:05 PM
              Subject: Re: [I-M223] 1000 GENOMES PROJECT
               
               

              A poster wandered far off topic to repeat gossip about Sen. Elizabeth
              Warren. Let's use that as a learning opportunity.

              Here's Warren's own statement:

              http://www.boston.com/news/politics/2012/senate/specials/elizabeth_warren_statement/

              This claim, "She was making this claim to meet diversity requirements
              at the universities where she taught...." is simply not true:

              http://www.washingtonpost.com/blogs/fact-checker/post/everything-you-need-to-know-about-the-controversy-over-elizabeth-warrens-claimed-native-american-heritage/2012/09/27/d0b7f568-08a5-11e2-a10c-fa5a255a9258_blog.html

              Back to Warren's ancestry. Here's a writeup about that:

              http://www.pollysgranddaughter.com/2012/09/elizabeth-warrens-reed-and-crawford.html

              It includes things like this:

              "Both the Reeds and Crawfords are ALWAYS found on federal census forms as
              white, going back as far as they can be traced on the federal census. They
              are white in EVERY other record they are found on as well. They are also
              found in NO Cherokee records, ever. Because the Delaware were adopted by
              the Cherokee Nation, from that time forward, they should be found in the
              Cherokee historical records if they were truly Cherokee or Delaware. They
              are not."

              Does that mean Warren was lying? No, it means she isn't a genealogist,
              and she believed what her relatives told her.

              "Both families are documented as white in all historical documents. Are
              we supposed to believe that there huge conspiracies in both families
              to cover up Indian blood and record themselves as white for as long as
              records have been kept in the United States? Or is it more likely someone
              along the way either got confused or made up stories about each of the
              families and now some descendants accept the stories as true?"

              Exactly.

              My grandmother was more curious, and turned into a genealogist
              because of it. Some people said her family was of Indian ancestry.
              Turns out we're descended from the *brother* of Creek Indian Chief
              William McIntosh. In this case, it was other people who said
              we were Indian, not family, but it was still a case of mythology
              being believed.

              And how about Henry Louis Gates, who was told by one DNA company
              that "his maternal ancestry could most likely be traced back to
              Egypt, probably to the Nubian ethnic group. Five years later,
              however, a test by a second company startled him. It concluded
              that his maternal ancestors were not Nubian or even African,
              but most likely European."

              Should he be slandered up and down the town for believing what a
              purportedly scientific company told him?

              On the other hand, I could list quite a few family stories from my
              family and allied families that turn out to be quite true, backed
              up now by genealogical research and in some cases by DNA.

              So, how about we give anybody who believes old family stories the
              benefit of the doubt, even if the stories turn out not to be true?

              -jsq

            • John S. Quarterman
              Dora, ... Indeed, the sentence I quoted and said was not true is not true. What you attempted to rebut was not what I said. ... Apparently you didn t even read
              Message 6 of 6 , Jan 22, 2013
                Dora,

                > Not true, huh?

                Indeed, the sentence I quoted and said was not true is not true.
                What you attempted to rebut was not what I said.

                > So if she's saying she didn't say it, she's lying.

                Apparently you didn't even read her statement.

                My point, once again, is that this is often the case:

                > "Or is it more likely someone
                > along the way either got confused or made up stories about each of the
                > families and now some descendants accept the stories as true?"

                Regarding Henry Louis Gates, it wasn't even his family that misled him:
                it was an apparently respectable DNA company.

                In the case of my grandmother, it was some descendants of related
                family groups.

                My grandmother spent many years researching the genealogy.
                Most people, as we all know, aren't that interested or don't
                have the time.

                I repeat:

                > So, how about we give anybody who believes old family stories the
                > benefit of the doubt, even if the stories turn out not to be true?

                And what it seems to me we are here for is to use DNA to try to find
                out what is true, as closely as the DNA lets us discover that.

                -jsq
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