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  • Michael Krakovskiy 2:34 am on March 18, 2009 Permalink | Reply
    Tags: 23andMe, AIDS, alpha, Anne Wojcicki, , , Bloom's syndrome, bone marrow transplant, cancer-causing chemicals, Classical genetics, co-founder, coughing, denied insurance, disease, diseases, DNA, e-ink, , , emacs editor, , genomics, genotype, , Haplogroup, Hemochromatosis, HIV, Human evolution, infection, , intercontinental travel, John Connor, , Lung Cancer, Lupus, Moyshe, , Parkinson's, Personal genomics, Population genetics, preservative solution, , , rare diseases, Sergey Brin, show Ankylosing spondylitis, Single-nucleotide polymorphism, SNP, strain,   

    A review of personal genomics profile from 23andme 

    What do I buy: a cleaning robot, an e-ink powered ebook, or a personal genetic test from 23andme.com? This is one of those terrible trilemmas facing geeks who are not willing to sacrifice financial stability for having all the coolest gadgets. I chose a 23andme test, and haven’t regretted it.

    The factoid that always is mentioned in the press about 23andme is that its co-founder Anne Wojcicki is married to Google co-founder Sergey Brin. This of course means that the data that 23andme is collecting is going to be used to help Google’s Skynet to gain the upper hand in the forthcoming war.

    23andme’s service works like this: you give them some money (at the time when I write this the price is $399, but it used to be over $800), they send you a test tube into which you spit, some special preservative solution, and a return envelope. You follow some simple instructions and send your spit to a processing facility. Then you wait (this is the hard part). In a month or so (it depends how long the backlog of orders is) you recieve an email telling you that you can log into 23andme.com and take a look at the results.

    The processing that they do in the lab creates a data file that represents an impressive number of genetic data points called SNPs or single-nucleotide polymorphisms. The way I understand it, SNPs are known variations that happen in DNA sequences. Much of the DNA stays the same for all people, but there are some variations in a single location. Let’s say there’s a string of DNA in humans that goes

    G-A-T-T-A-C-A
    C-T-A-A-T-G-T

    and 6 positions there are the same for everyone, except the seventh, which is sometimes AT and sometimes GC. So basically it’s a single position on the one of the 23 chromosomes or mitochondrial DNA (I guess 23andmitochondriaandme was shot down as a possible name for the company) that statistically is different from person to person as opposed to long stretches of DNA that stay the same.

    Scientists all over the world are studying the correlations that SNPs have with disease risks and traits. I guess these studies go something like this: you grab 500 programmers that use emacs editor and 500 that use vi. You have a hunch that editor preference is related to gene C4711. You sequence the dna of all your coders looking for SNPs in the gene C4711 that are one way in your vi-using alphas and another way in emacs-using sub-omegaloids. Then you find that in most of vi users SNP rs1729 is AA. Then you come out and say – AA in s1729 increases the odds of a programmer preferring vi by 47%.

    The more people that a study has – the better the results. 23andme has genetics experts on staff that sift through mountains of these studies, rank them, and then tell the website people to add results to the interface. This way you can go to 23andme.com and see (as of right now) that tell you right away what your lifetime chances of getting 10 diseases. Some, like Parkinson’s, they don’t let you see without you agreeing to see it yourself. Sergey Brin was reported in the media to get some bad news from that particular one (mine came back “Typical Risk” which means that my chance of getting Parkinson’s is about 1.6%, same as everybody else).

    A lot of people that I talked to about genetic testing told me that they’d “rather not know”. It’s true that some of the things that you might learn will make you worry without being able to do anything about it. On the other hand, there are some that you might be able to do something about.

    “24.1 out of 100 people of European ethnicity who share this genotype will get Prostate Cancer between the ages of 35 and 79” vs “17.8 out of 100” on average. Here I learned that I have about 1 in 4 chance of getting prostate cancer. Prostate cancer is one of the relatively treatable ones if caught early, but with unpleasant diagnostic procedures. All of a sound “digital exam” does not sound so bad, and I guess I’ll have to bend over and cough a lot more often than I otherwise would. I’m not sure what coughing does, but the “digital” part has nothing to do with electronics or numbers.

    There are also 10 traits that are available right now. The most interesting one for me was “Resistant to infection by the most common strain of HIV people usually encounter, though protection is not complete”. I apparently have two copies of something called “Delta32 version of CCR5”. “Although people with two copies of Delta32 are highly resistant to the most common type of HIV, they can be vulnerable to strains of the virus that do not use CCR5 to enter immune cells”.

    This makes me a little bit more at ease when I donate blood, even though I know that the chances of getting infected with AIDS at a blood donation are already less than winning that Mega jackpot. On the other hand Dr. Asimov died of AIDS that he received through a transfusion. What’s more interesting, is that this is the same mutation that prominently figured in the media with the AIDS patient who was cured through a bone marrow transplant.

    Then there’s a section that has 79 research reports. These get a rating fоr “research confidence”. I, for instance, have an elevated risk of obesity from research that has a three star rating.

    Doctor House would have loved getting access to this kind of data for every one of his patients. There are risks for rare diseases mentioned on the show Ankylosing spondylitis, Hemochromatosis, Bloom’s syndrome, and everybody’s favorite – Lupus (which it’s never).

    One of the tests included in 23andme is for muscle performance, the one that was in newspapers lately because it was offered by a few companies. The news angle was that sports obsessed parents paid hundred of dollars to find out if their kids have sprinting or marathon ability. Mine says: “One working copy of alpha-actinin-3 in fast-twitch muscle fiber. Many world-class sprinters and some endurance athletes have this genotype.” This sounds plausible – for a fat dude I have an uncanny ability to sprint, yet suck at long distances.

    But wait, this is not all. For the same low price you also get some ancestral info. This comes in a form of maternal and paternal haplogroup. I am not sure I understand the what haplogroup is very well, and found 23andme’s infographics somewhat confusing. From what I understand a haplogroup is a number that is attached to a certain mutation (a few SNPs maybe?) that arose thousands of years ago and that has been statistically crosslinked to people living in certain geographical locations.

    My paternal haplogroup is E3b1c1* – “populations: Ethiopians, Jordanians, Ashkenazi and Sephardic Jews”. My maternal haplogroup is H5a* – “populations: Lebanese, Polish, Irish”. Both of my ancestral branches are supposedly Ashkenazi, and I guess haplogroups are not a high enough resolution to prove or disprove Jewish ancestry. All they do is tell you that the progeny of your very remote ancestor was likely found in certain wide geographic locales “before the era of intercontinental travel.” What’s interesting is that there’s a small chunk of my maternal haplogroup’s population in Siberia.

    23andme is a true Web 2.0 service (in the good sense of that expression). There’s a blog called The Spittoon. In between educational (sometimes interesting, sometimes boring) posts about genetics they have a section called “SNPwatch“. There they write about new research and usually provide a link to raw data in your 23andme profile. So for instance there was an article titled “Variants in Genes for Carcinogen Transporters Linked to Lung Cancer” about a mutation that prevents lungs from clearing out cancer-causing chemicals. Then you can click on two links and see if you have that mutation (to my relief I don’t).

    There are some social network features: you can compare your DNA profile to your relatives. I’m not sure if hilarity might ensue because I think you can figure out possibility/impossibility of paternity and maternity, like Dr. House did in that episode. You can even compare your DNA to other users of 23andme – you have to accept a “friend” request for that. I’m not really sure what’s the fun in that. You can participate in surveys that might be used for research (there isn’t one yet about vi vs. emacs yet, but there are some other ones).

    It does not look like the $400 fee even covers the cost of gathering the data (there no further fees as of now) or paying for staff/website maintenance, and ongoing research. I’m not really sure what the business model here is (and that makes me a little nervous. Businesses like this remind me of an old Yiddish joke:

    Moyshe is selling boiled chicken eggs. He buys them for a kopek each and sells them for a kopek each. Chaim asks – “Moishe – where’s the profit in this?” “What, are you stupid?” – answers Moyshe. “I get to keep the broth”.

    My guess is that the “broth” here is an opportunity to conduct groundbreaking research and maybe sell the anonymized data. That, and helping Google’s Skynet find and assassinate John Connor.

    I don’t really worry too much about being denied insurance in the grim meathook future that surely is coming just because I used 23andme. There’s legislation against that on the books right now, and if insurance companies will be able to deny coverage based on genetics they’ll be much more likely to get this info by requiring a blood test.

    I really wish I could get the data from my grandparents (none of whom are sadly alive). I will buy kits for my entire family though as soon as I’ll be willing to part with another chunk of disposable income (I do want that dang Kindle first though).

     
  • Michael Krakovskiy 5:05 am on July 28, 2008 Permalink | Reply
    Tags: alpha, , Brain Surgeon, , fatal infection, Firlik, Frontal lobe, fully qualified surgeon, Lobe, , , neurosurgeon, primitive tools, superbly gifted writer, , trained scientist, untreated earache, young roofer   

    Another Day in the Frontal Lobe: A Brain Surgeon Exposes Life on the Inside 

    Katrina Firlik is a neurosurgeon, one of only two hundred or so women among the alpha males who dominate this high-pressure, high-prestige medical specialty. She is also a superbly gifted writer–witty, insightful, at once deeply humane and refreshingly wry. In Another Day in the Frontal Lobe, Dr. Firlik draws on this rare combination to create a neurosurgeon’s Kitchen Confidential–a unique insider’s memoir of a fascinating profession.

    Neurosurgeons are renowned for their big egos and aggressive self-confidence, and Dr. Firlik confirms that timidity is indeed rare in the field. “They’re the kids who never lost at musical chairs,” she writes. A brain surgeon is not only a highly trained scientist and clinician but also a mechanic who of necessity develops an intimate, hands-on familiarity with the gray matter inside our skulls. It’s the balance between cutting-edge medical technology and manual dexterity, between instinct and expertise, that Firlik finds so appealing–and so difficult to master.

    Firlik recounts how her background as a surgeon’s daughter with a strong stomach and a keen interest in the brain led her to this rarefied specialty, and she describes her challenging, atypical trek from medical student to fully qualified surgeon. Among Firlik’s more memorable cases: a young roofer who walked into the hospital with a three-inch-long barbed nail driven into his forehead, the result of an accident with his partner’s nail gun, and a sweet little seven-year-old boy whose untreated earache had become a raging, potentially fatal infection of the brain lining.

    From OR theatrics to thorny ethical questions, from the surprisingly primitive tools in a neurosurgeon’s kit to glimpses of future techniques like the “brain lift,” Firlik cracks open medicine’s most prestigious and secretive specialty. Candid, smart, clear-eyed, and unfailingly engaging, Another Day in the Frontal Lobe is a mesmerizing behind-the-scenes glimpse into a world of incredible competition and incalculable rewards.

    From the Hardcover edition.

     
  • Michael Krakovskiy 5:16 pm on July 26, 2008 Permalink | Reply
    Tags: Acclaimed photographer, , , Adobe Photoshop version history, , alpha, , Black and White, Digital Imaging, , Director of Engineering, , , image processing, internationally renowned photographer, , Marc Pawliger, Martin Evening, , , Professional Image Editor, , Raw image format, raw image processing controls, Scott Kelby, , the black and white conversion tools   

    Adobe Photoshop CS3 for Photographers: A Professional Image Editor’s Guide to the Creative use of Photoshop for the Macintosh 

    Master the power of Photoshop CS3 with
    an internationally renowned photographer by your side.

    Adobes Photoshop CS3 comes with powerful new features with huge payoffs. But it can be overwhelming to learn, even for professional photographers, graphic designers, keen amateurs, and others who already have an initial grasp of Photoshop. Acclaimed photographer Martin Evening, who wrote the best-selling previous books, ‘Adobe Photoshop for Photographers’, makes it easy with this new, thoroughly updated edition.

    * Illustrated throughout with before-and-after pictures more than 750 professional, color illustrations!
    * Practical techniques and real-life assignments
    * Step-by-step tutorials
    * Keyboard shortcut reference guide

    Includes FREE DVD with:
    * QuickTime movie tutorials for MAC and PC
    * Searchable tips on tools, palettes layer styles, and shortcuts
    * Includes images selected for you to experiment with to get you up to speed with everything in the book, including the new Photoshop CS3 features, fast!
    * Updated Camera Guide to help you decide which will best suit your needs, plus bonus Digital Capture chapter in printable PDF format

    Uncover quickly exactly what Adobes CS3 now offers photographers. New tutorials focus on the key features introduced in CS3. You lose no time in finding out how to put your ideas to work with:

    * Adobes Camera Raw 4 plug-in that can now also process TIFFs and JPEGs
    * New Align controls for combining HDR images; Photomerge; new Clone Stamp; Curves dialog that now incorporates Levels functionality; and improved controls for Brightness/Contrast to match raw image processing controls
    * The latest on Black and White adjustment, which provides all the black and white conversion tools you need for optimum monochrome conversions
    * A pros scoop on choosing from among dozens of Photoshops image adjustment methods to get the results you want
    * Tips on Bridge 2.0 and Lightroom when you should use each
    * Top tactics for successful composite images, insider guidance on editing shadows and highlight adjustments, and lessons on how to preview and re-edit filter effects as many times as you want without complex workarounds

    Get the preeminent advice from one photographer to another as Martin completely updates you on the core aspects of working with Photoshop, digital workflow, and improving accessibility. Real-life examples, diagrams, illustrations, and step-by-step explanations ensure that youre up to speed with the next generation of digital photography in no time!

    Foreword by Adobe Systems’ key Director of Engineering, Digital Imaging, Marc Pawliger

    * Over 750 professional, color images make this book stand above the rest
    * New DVD! Searchable info explains tools, palettes & layer styles, also includes invaluable QuickTime movie tutorials
    * Master the power of Photoshop CS3 under the instruction of an internationally recognised Photoshop expert & Adobe alpha tester

     
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