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).

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.

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
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* Illustrated throughout with before-and-after pictures more than 750 professional, color illustrations!
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* 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:

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Developer Life, Yo

These days there are a lot of documentary shows on TV about various professions. I am somewhat addicted to them – I watched whole seasons of shows about hairdressers, crab fishermen, lobster fishermen, tattoo artists in Florida, tattoo artists in Nevada (but not the one about tattoo artists in LA), restaurateurs ice road truck drivers, custom motorcycle builders, custom car builderscorrectional officers and inmates, and the Philadelphia meter maids.

My own profession is mostly untelevisable. Mostly. Well, maybe some TV network might make a show out of Aardvark’d: 12 Weeks With Geeks. I also think that there could be a tiny market for a heavily edited “looking over the shoulder” video on the code writing habits of colorful  alpha geeks like Linus Torvalds, Donald Knuth, Brad Fitzpatrick, Dries Buytaert, and maybe even  JWZ. I’d buy that for a dollar.

I found that there are two occupations that are unexpectedly similar to that of a software developer: prison inmate and line cook. Both of these are heavily male dominated, involve a disproportionate amount of minorities and are very stressful.

I recognized offices in which I worked all my life in prison layouts.  The common criminals usually live in a common area in the center of the prison. This is exactly like a common area of an office, except with bunk beds instead of desks. Some actually have semi-private cubicles. Inmates organize into gangs, just like departments. Gang leaders are usually placed into single or double cells that line the perimeter of the common area to cut down on the communication between them and their reports.  Even there you have to be a manager to score an office.

Restaurants are a lot like developer shops. You have your front of the house: waiters (sales people),  hosts and managers, food runners (analysts). And then you have your back of the house: chefs (architects and lead developers), line cooks (developers) and  prep cooks (producers). There’s no good equivalent for dishwashers in a typical developer shop.

People often assume that a chef primarily cooks and a lead developer primarily codes. Do you know the title of Julia Child’s awesome show? Well, she was neither French nor a chef. Chefs do surprisingly little cooking, they are more like conductors in  orchestras. They create menus,  divvy up the tasks, check quality, train and supervise cooks.  Best chefs, just like the best lead developers do find time to cook, but still spend more time organizing, tasting and researching.

There are Always Leaks

There are those movies that keep you actively thinking about them for days and weeks after you see them. Primer, which I watched with my wife yesterday is one of those. If you are one of those who are afraid of “spoilers” – this is your warning, although I believe it’s really impossible to create a “spoiler” for this movie. You’ll watch it once, twice, three times, then with director’s commentaries, then read the entire message board and still will not be able to figure it out entirely.

Primer is a story about time travel paradoxes, but not really. It’s about innovation, competition, trust and inability to see the entire picture.

Without the science fiction element, the movie is about garage innovators. The core of innovative group is almost always two people. Sometimes it starts out with more people, but then boils down to two. Jobs and Wozniak, Hewlett and Packard, Gates and Allen. You need to have your John and your Paul, George and Ringo are not that important. So you have these two people who together are destined to create great things. Can they trust each other? Would they do screw each other over?

We know for a fact that the alpha geeks are often ruthless. Steve Jobs gets a design job from Atari, gives it to Steve Wozniak, promising 50/50 spilt, and after Woz delivers the work gives him $300 while pocketing a few grand, saying that the fee was $600? When Apple becomes a success he deserts Wozniak. Then gets forced out himself. Then he majorly screws over founders of Pixar. Then takes back Apple. Typical preppy high school drama, except with higher stakes. And realize this – he does all that instead of enjoying his money and free time.

Anyway, the movie has two protagonists, Abe and Aaron, engineers talented like Woz and a bit less ruthless than Jobs. Abe creates a time machine that can use to travel back in time to the moment when the machine is powered up for the first time and then explains its use to his friend. That opens endless possibilities for them: make money in the stock market, prevent bad stuff from happening. Which they do for a while, but then their competitive instincts kick in. Can you really trust your partner not to go into the past and put you out of commission?

Worse of all — if you go back in time and then prevent your second self from entering the time machine all of a sudden there are two of you. The biblical names of the characters are significant in this context – Abraham – the “Father of Many” and Aaron – the “Bearer of Martyrs”. They become involved and a four-dimensional battle for control with each other and their paradox-born doppelgangers. “Failsafe machines” — extra time boxes set up in hidden locations that allow for extra “entry points” or “save points” become important weapons in this game. Can you really trust yoursef becomes the real question.

Abe and Aaron are competitive and very, very smart. They create a crazily complicated situation, with time machines, time machines inside time machines, doubles that have all recorded audio track of the timeline provided to them by future selves, extra timelines and resets via failsafe machines. “Are you hungry? I haven’t eaten since later this afternoon” sounds absolutely normal in the context.

A similar, buth much less complicated situation transpired in Stanislaw Lem’s 7th voyage of the Star Diaries of Ijon Tichy..

That sci-fi story went like this: Ijon’s rocketship ends up in a “space storm” with a broken rudder. Fixing a rudder is a two person job, but luckily the space storm brings together Ijons from different times. All he really needs to do is put on a space suit, wait for a later him wearing a space suit to appear, cooperate and fix the rudder. Instead he ends up arguing with his future and past selves, hitting and being hit by them and eating his own supplies of chocolate. Here’s a quote from what seems to be a full text of the story that somebody probably illegally posted on the web:

“I came to, sitting on the floor of the bathroom; someone was banging on the door. I began to attend to my bruises and bumps, but he kept pounding away; it turned out to be the Wednesday me. After a while I showed him my battered head, he went with the Thursday me for the tools, then there was a lot of running around and yanking off of spacesuits, this too in one way or another I managed to live through, and on Saturday morning crawled under the bed to see if there wasn’t some chocolate left in the suitcase. Someone started pulling at my foot as I ate the last bar, which I’d found underneath the shirts; I no longer knew just who this was, but hit him over the head any how, pulled the spacesuit off him and was going to put it on–when the rocket fell into the next vortex.

When I regained consciousness, the cabin was packed with people. There was barely elbowroom. As it turned out, they were all of them me, from different days, weeks, months, and one–so he said–was even from the following year. There were plenty with bruises and black eyes, and five among those present had on spacesuits. But instead of immediately going out through the hatch and repairing the damage, they began to quarrel, argue, bicker and debate. The problem was, who had hit whom, and when. The situation was complicated by the fact that there now had appeared morning me’s and afternoon me’s–I feared that if things went on like this, I would soon be broken into minutes and seconds–and then too, the majority of the me’s present were lying like mad, so that to this day I’m not altogether sure whom I hit and who hit me when that whole business took place, triangularly, between the Thursday, the Friday and the Wednesday me’s, all of whom I was in turn. My impression is that because I had lied to the Friday me, pretending to be the Sunday me, I ended up with one blow more than I should have, going by the calendar. But I would prefer not to dwell any longer on these unpleasant memories; a man who for an entire week does nothing but hit himself over the head has little reason to be proud.”

One other main themes of the movie is the inability to know certain things no matter how smart you are. Too many things are open to too many interpretations. The geeks on the web are obsessively putting together timelines, diagrams and theories of what really went on. I don’t even think that the author of the screenplay completely understands the whole sequence of events. And he directed and played in the film! How many timelines are there? How many Abes and Aarons? What do they mean by “recycling” the machines? What the hell happened with Tom Granger?

There is also an interesting recursive theme in the movie: cheapness. The actor/director/screenwriter, shooting on what is described as $7000 budget and making it look very good, has done some ingenious things. So do the inventor in the movie – he keeps his day job instead of throwing it away to follow the dream, too cheap to have a steak for lunch, and even at some point he cuts copper tubing needed for the project out of a refrigerator. I don’t know if building a time machine is that much more difficult than making such an awesome movie on a 7K budget.

By the way, if you are looking for hints about the movie, the commentary track on the DVD is a pretty horrible place to start. It’s full of jems like “That sound effect – yeah [background laugh] – that was George Forman Grill”.

All I know, is that I want an Emiba Devices t-shirt. And a garage.