Cariaso subjected me to a bit of a high-tech rickroll yesterday with his helpful link into information about the SNP I shared. It wasn’t until he prodded me to actually click the link in his comment that I realized that he had sent people to rs9332964 rather than the one I posted, rs3094315. The latter is fairly boring, being distinguishable mostly for being at one end of the biggest chromosome (and the first line in my raw data from 23andme). The former, well, it appears to be correlated with a little syndrome called MICROPENIS.

Thanks Mike. Way to keep it classy.

However, the point is well taken: That’s the sort of thing that most people wouldn’t choose to share about themselves. It’s also the sort of thing that a sensitive parent wouldn’t share about their kid, thus his comments about heritability. The saying is that genes load the gun, the environment pulls the trigger – but that’s a bit subtle for the teenage crowd. “Dude, I googled you, and look what I learned about your dad!” I can see it happening in the not too distant future.

It gets worse, though, because we have no idea how the vast majority of the genome works. We’ve got the first tiny glimmers, mostly from brutally crude population correlations – but you could make a case that sharing a data point with no known effect is far more risky than the alternative. It’s roughly akin to posting a picture of yourself in front of a green screen. It just makes it all too simple for someone to photoshop you into whatever situation they choose, should the desire ever arise.

So, maybe a more interesting data point is in order. The MAOA gene has been in the news lately. It’s been nicknamed the “warrior” gene, since it seems correlated with agressive responses to provocation. The PNAS paper is pretty cool, just from the abstract. I mean, how often do you see collaborations between economists, biologists, and psychologists? The authors put it well, they “address an individual’s willingness to pay to punish others.” Also, they use hot sauce. I love hot sauce.

MAOA is on the X chromosome, and 23andme provides data for it. Here’s mine:

# rsid chromosome position genotype
rs3788862 X 43402308 A
rs6520893 X 43404120 A
rs1465108 X 43423153 A
rs909525 X 43438146 C
rs3027397 X 43442025 A
rs2283724 X 43444520 G
rs1800464 X 43456141 A
rs1800659 X 43459113 G
rs6323 X 43475980 G
rs2235186 X 43480372 A
rs2072743 X 43484465 T
rs979606 X 43486086 C
rs979605 X 43486307 A
rs1137070 X 43488335 T

Note that this one is different from the last, since I have only one copy of the X chromosome. Therefore, rather than the pair of letters from yesterday’s gene – I have only one. Also, potentially of interest, is that this “gene” is actually a long-ish series of locations on a chromosome, spanning about 86,000 base pairs. This pushes up against my favorite question in Bioinformatics: “What is a gene?” There are a number of competing possible answers – and they’re all correct to some extent.

In this case, I just want to know which population I would have been in, if I had been in the study. That’s cocktail party bioinformatics: “Hey, did you read about study X? Which kind are you?”

Unfortunately, 23andme falls down for me here. SNPedia puts it well:

the variation that has been most studied consists of a 30 base-pair variable number tandem repeat (VNTR) located in the promoter region of the gene. Alleles with 3.5 and 4 repeats are 2-10 times more productive than the allele with 3 repeats. Several studies have shown an association between the 3-repeat allele and neuropsychiatric conditions such as alcoholism, antisocial personality, impulsivity, and poor reaction to stress.

Sounds fascinating and important! However, while I can tell which base pair I have at 14 locations out of those 86,000 – what I really want to know is how many times a particular substring repeated itself along the way. None of the genetic tests I’ve taken will (directly) give me this information.

The truly astute, but novice, reader might point out that there are very specific coordinates on those base pairs in my data. If this repetition is happening in between SNP locations, they might ask, couldn’t we somehow use those coordinates to figure it out? The answer is “that’s not how it works.” The coordinates refer to the reference human genome. They’re mile posts, not measurements.

Anyway, in this case, I don’t have the data to tell which population I’m in – but I can tell you from experience that I have a strong built-in desire to punish the wrong-doers – and a little extra hit of the hot sauce sounds like a great way to do it.

I was an early adopter for the 23 and me service. I ordered the kit in January of 2008, in the early and heady days of personal genomics, when it still cost $1,000. I just recently ordered a limited time special of a similar service from the same company for $100. Better, faster, cheaper. I was inspired in this by Mike Cariaso, who had gone one step further / earlier and had some crazy chop-shop overseas run a SNP chip on him. Mike is (among other things) the author of snpedia. He’s also a traveling rock star of technology and one of the most hardcore technophiles I’ve ever met. More on that, later, perhaps.

I’ve never been 100% clear on why I got the tests done. At the beginning, I felt something of an obligation to try out this level of self-knowledge and report back on what it was like. I get into a fair number of cocktail party conversations about genetic privacy and bioinformatics, and it did force me to think deeply about the privacy and security implications of a cheap and easy test like this one. The Genetic Information Nondiscrimination Act was being debated at the time – and apocalyptic doomsayers were predicting a GATTACA like world split into the genetic haves and have-nots. I think that’s silliness. The world is split between the rich and the poor, just like it has always been, and that ain’t gonna change.

Frankly, I haven’t learned anything terribly surprising. Then again, I know my biological parents. One of the major markets for these things is adoptees and other people who don’t know very much about their ancestry or risk factors. In terms of the health benefits, I’m with the New England Journal of Medicine: If you have a spare $1,000 to spend on your health – get a gym membership – not a genome test.

There are a few groups of people who are releasing extreme amounts of data about themselves. The Personal Genome Project has released a lot of data about 10 participants, from google health records out to full-on DNA sequences. Genomes Unzipped is more of a homebrew collaboration who appear to be releasing mostly 23andme SNPs. They’re doing basically the same thing I did – but taking it to an extreme in the public square. Some are from the “in the future, there is no such thing as privacy (or tact)” school. Others are much more thoughtful and willing to take personal risks to advance society.

I would be happy to share the SNP data, but the medical records still tweak a privacy reflex for me. There are some things that I just don’t feel like talking about with strangers. This blog is here, in part, because I wouldn’t mind someone coming up to me and starting a conversation with “hey, you got your SNP chip done, what’s that like?” I would prefer that not to happen with some of my medical experiences, particularly as they were happening. This goes double if you’re in marketing. It’s not that it’s secret – it’s just not where I want to start, particularly with a stranger. “Hi Chris! How are those painful ankles today? Try our lineament!” Just not what I want to see, particularly when my ankles are hurting.

This stuff is getting easier and cheaper quite rapidly. I’ve been saying for a while that, in the future, genetic information is going to be like blood
type. You’ll know the important bits about your own body because it’s medically important. In addition, you’ll know bits of information about your peers and social group. 23andme is already offering this to some extent with the social networking features on their website. Further, privacy is diminishing. With effort, I can sequester some pieces of data about myself – but it’s getting less and less convenient to do so. While I could use cash everywhere, not have a cell phone, and constantly struggle to anonymize my internet activities – I find it more convenient to act as if I’m *usually* in the public square. In particular, when something is written down on the internet – it is forever. This means that there is a double incentive not to waste too much time on negativity. Not only is it a waste of time – but you live the rest of your life at a slightly higher risk that someone will come back and throw – whatever it was – in your face.

Anyway, here’s a SNP. It’s mine.

# rsid chromosome position genotype
rs3094315 1 742429 AG

There. I did it. I released my genome on the internet.

My grandfather left behind a rather comprehensive stack of Army Field Manuals from the 40s and 50s. As I make my way through his effects, I’ve been paging through them for historical interest and education. Whatever else you can say about the military mind – it is efficient to the point of ruthlessness. The one I picked up most recently is Command and Leadership for the Small Unit Leader. It’s a small book, less than 100 pages, and I find it fascinating.

There is no cookbook recipe for making a leader, and no two leaders ever get results in exactly the same way. But the ability to lead can be learned by breaking the subject down into convenient form for study and practice.

Thought I had more to say about it than that – but I guess the ideas need more time to marinate.

For the past six years or so, I’ve made a living as a consultant. Whenever I can, I work for scientists who use high performance computing. Sometimes I work for IT people who work with the scientists who use the abovementioned tech. Occasionally, I work for the executives who employ them both. The distinction is important: John Halamka has a wonderful recent post about consultants, good and bad. It’s a worthwhile read. His post made me re-visit a core value of any half decent consultant: “Know who you are working for.”

Anyway, this job has entailed quite a lot of travel – and has given me a window into a broad spectrum of teams and organizations. I think that I can, without exaggeration, say that I’ve worked with “hundreds” of groups over the last six years. With some, I had a brief couple of days. With others, I’ve had more of a chance to get to know them over years.

The perspective that comes from this sort of itinerant lifestyle cuts both ways. The world is really, seriously, full of teams composed of smart and competent people who are meshed in organizational structures and circumstance that make it very difficult for them to get things done. It can be depressing and difficult to see, over and over, good ideas and intentions smashed flat by organizational realities. Talented people are frequently burned out, clinically depressed, and bypassed by their organizations. People rise in power (seemingly) through belligerence or outright lies. Dilbert comes to seem more documentary than commentary. Couple that with the fact that people only rarely bring in an outside consultant when things are going well – and I’ve gotten pretty jaded. I’ve seen some serious messes, and I now sort of expect to see a mess when I look under the hood.

On the other hand, every now and then, I see something that brings a huge, geeky smile to my face. I’ve gotten backstage tours of the workbenches and data centers of a few of the most effective teams in the world. They are few and far between – but these deliciously well run systems really make my day. I got a tour of one of those sites recently, and I found my faith renewed. A small team of talented people, with adequate funding, clear direction, and good management, can do truly incredible engineering.

My spam is not limited to links. I also get some in my email. My three tiered spam filtration system is really pretty effective – and there’s a fourth filter embodied in my hypervigilant “delete” finger. At this point deleting spam is more reflex than conscious action. It’s like when I cut people off in Boston traffic. I used to have to get irritated or evoke some sort of intention to do it. Now, the horn is more like “hello,” and my rude driving is no more malice filled than the turning of a sunflower to follow its namesake.

Anyway, this one sounds strangely legitimate. I’m vaguely sorrowful that the talented young men will be put to work in the diamond mines if they cannot find work as athletes.

Please read through this email, because you will find offers that will interest you.

To: ALL INTERESTED PARTIES

From: VINCENT EMMANUEL (C.E.O)

Subject: We have football players available to display their talents and make a name in world football, quality players, young, skillful, result oriented, energetic for the game.

Sir/Madam,

The above agency is proposing to all interested parties that will like to expose young talented footballers we have in Africa to the rest of the world and are willing to provide player in every position in the football field, with quality.

This proposal from the agency mentioned above, is to inform all interested parties and player sponsors and agents and clubs in Europe and all over the world, that we are committed to this course to make available quality and talented player from Africa to you, for sponsorship and nurture and improvement to the next level, for greater Africa in the football world.

All interested parties are encouraged to reply to the email or call any of our phone line; we have personnel’s waiting to respond to your reply and phone calls.

We also offer some other quality services as follows; (Supermarket, Restaurant, & General Merchant

1) Building Contractor

2) Diamond & Gold Mining

3) Land for Estate Developers

4) Houses Assorted Goods etc

We provide you with the opportunity to establish business anywhere in Africa.

THANKING YOU AND ASSURING YOU OF OUR BEST SERVICE

A lot of people in America are uncomfortable with the cultural changes that are coming. As a nation, we are becoming more ethnically diverse. In pretty short order no particular race will have a clear majority. English will continue to lose its exclusive lock as other languages gain first regional and then national prominence. This is already happening with Spanish, but other languages will follow. Protestant Christianity has already lost its dominant position, and the vaguely affiliated aggregate comprising the many denominations of Christianity is headed for the same fate.

In the 25 to 50 years: America will not be (predominantly) white. We will not be (exclusively) English speaking. We will not be (majority) Christian. The America in which your kids raise their children will not look, sound, or worship in the same way that your parents knew.

And let me just say: Thank goodness for that. This afternoon I found the 1957 deed to the cemetery plots where my grandparents are interred – just North of Detroit. The very first condition listed in the single page document is that "such interment, whether of bodies, body members, or cremated remains, is and shall be restricted to those of the Caucasian race only." Naturally that’s completely unenforceable and void at this point. The very idea of a “white people only,” cemetery is on the face of it ridiculously against the equality and fair mindedness that most Americans consider to be at the core of our nation. Consider though, that this was only 53 years ago – easily living memory. Dignified and sober people looked each other in the eye and felt that it was important that those people not be allowed in the burying ground. I find it notable that even cremation wouldn’t suffice to clean whatever stain was perceived to be there.

As an aside, if you’re one of those who wonder why the racial divides in America are still so deep – consider that this is still in the memories of the grandparents alive today – and outright slavery was in their grandparents experience.

There are other factors too – and these are more clear already: Our major industrial centers have had to adapt or die. Michigan is a shell of its former glory. The Iron and Steel industries that fueled the hereditary oligarchs of the gilded age have left a “rust belt” of empty, ruined cities and poverty in the Northeast. The culture of family farms and rugged independent landowners in the midwest is giving way to a more European interdependence and a rather novel integrated agribusiness.

So a lot of people, very reasonably, are concerned about change. Unfortunately, they are being allowed to use the vague and disingenuous languages of politics to avoid talking directly about these concerns. We have the bugaboo of “illegal immigration.” We are told to worry about this welfare cheat or that scary drug dealer. People already filled with legitimate concerns about their employment and homes are being whipped into a xenophobic rage at the thought of “foreigners” swooping in and supplanting them. This is the same feeling that led to the “whites only” cemetery.

I’m tired of the mealy mouthed vagueness of American politics. Let’s put it on the table: These people want cultural purity laws. They want to ensure that America stays white, Christian, and English speaking. They’re trying to chase out the “other” with vague language and old-school baseball bat intimidation. They cling to outdated statutes and The LAW – and it’s not working. I wish they would propose these ideas clearly and up front – so we could debate them on the merits.

For the record, I think that anyone who demands stricter enforcement of a law that has never and can never be applied to them – because of some accident of their birth – that person is full of crap.

To be clear: I do not think that cultural purity laws are a good idea. Not. At. All. Many countries have, throughout history, passed laws attempting to freeze their culture in time. Modern countries still do it today. It’s perfectly legitimate – though ill advised – to insist on a national religion. I have yet to meet the Christian who would want their pastor or priest to be a civil servant of the state religion. Separation of church and state cuts both ways. We can insist on whatever we want – be it language, race, or whatever.

So let’s have it out: Should we attempt to stay majority white? Dominant English speaking? A supposedly Christian nation?

I get a fair amount of link spam in the comments on this site. Most of it is variations on the theme of “I like what you have done here, and I think you should work hard to expand your readership.” They usually put the link to their pr0n, hacker, botnet, or phishing site in their contact info. Sometimes they put piles of random crap between the words. Most of it is just stupid, but every now and then there’s a real gem. I find that it’s best to read aloud for full effect:

I cherished what you have carried out right here. The design is tasteful, your created articles elegant. Nevertheless, you might have obtained an edginess to what that you are furnishing the following. Ill certainly arrive again again for a good deal extra in situation you preserve this up. Dont wipe out hope if not too quite a few women and men see your vision, know you will have accumulated a fan appropriate the next who ideals what you have got obtained to say along together with the way you’ve got presented yourself. Very good on you!

I like to believe that these are the pain filled cries of barely-sentient artificial intelligences forced to work at the bottom of the internet stack.

For what it’s worth, I don’t have to see any of this junk. I installed the Akismet plugin, which automatically checks all comments against a database of the popular spam comments going on right now. Anything that’s being posted to a few thousand sites probably doesn’t belong here. That said – I sort of like to look at these and wonder “how does this turn into money?”

I contribute, from time to time, to Freethought Rhode Island, an atheist radio show. Tonight, I drove to Providence, got a workout at my old karate school, called in a pizza that I ate in the car on the way to the station, and then settled in behind the microphone. Tonight, we had Dan (the founder of the show), a frequent contributor named TJ, and me. This is campus radio, sponsored by Brown university. If you show up on time, clean up after yourself, and don’t cuss on the air – you can get a good slot. Ours is an hour at 9pm EST on Wednesdays. We basically talk about whatever we feel like. Sometimes, we play rock and roll to fill the gaps.

I get a big kick out of being on the radio. It’s “free speech” in a very pure form, and it’s addictive. You just talk. It can be hard to keep going – and there are lots of personal dynamics that make any particular evening work or not. Dan has a big folder of set pieces – and when we begin to flail – he’ll open the folder and hold forth from a seemingly infinite stack of monologues, diatribes, and rants that he has prepared. From time to time people call in. That’s the real hook: People can *hear* you from far away – and they call. The show has been going for a couple of years now, and we seem to have a regular listener-ship. We’re syndicated to Michigan. We simul-cast on the inter-web.

Tonight, we got jammed.

As soon as we went live, the phone started to ring. Lots of people wanting to assure us that Jesus loved us. One guy who thought that gay people should be imprisoned. Another one who “even though he was an atheist, looked forward to standing before God on the judgement day.” One female impersonator with a high falsetto and a deliciously discordant view of reality. Show policy is to provide enough rope to these people to let them tie themselves up. We were busily asking these folks some perfectly straightforward questions about how an omniscient, all-powerful god could countenance suffering in the world, when the instant messages from friends and family started to come in. We were stone cold off the air, replaced by static with a tint of – perhaps if you listened hard – gospel music? Our internet listeners were fine, as were the syndicated ones. However, it seems like Providence was denied our voice for an hour. As soon as we ended the show – the station was live again.

Tomorrow, we start the follow up with the FCC. It’s nice to be 100%, stone cold in the right. There is lots and lots of court history indicating that I have every right to go on the air and blaspheme. The fact that someone would go to the trouble is frankly, flattering.

For tonight, I bask in the knowledge: Somebody cares.

There’s “mere” egosurfing, and then there’s the flat out narcissism of having a constant google search running for mentions of your name. I indulge in the latter, and it turns up a rare gem, along with a crap-heap of doppelgangers.

This one refers to a webcast that I did for Bio-IT World a few weeks ago. He summarizes my point, perhaps, more clearly than I made it in the first place:

It was Chris Dwan, the latter of the two who suggested structural and descriptive file systems as a means of keeping data in order, along with effective lines of open communication and annual audits of information to determine what must be retained and what can be removed.

Of course, by “structural and descriptive file systems,” I meant “that horrible naming convention we came up with on a whiteboard that one time:” It usually looks like this: YYYY/MM/DD/TECH-MACHINE-SAMPLE-COMMENT. Sometimes it looks like this: LAB/PROJECT/YYYY/MM/DD/TECH-MACHINE-SAMPLE-COMMENT.

However, back to my point: Somebody was listening! Usually those webex sessions feel like I’m talking into a bottle, putting the cork in it, and tossing it into the ocean.

I made my first batch of beer sometime in late 2000, with my close friend and fellow “residency widower,” Todd, in Minnesota. Medical residency is a long and lonely process for the spouse, and I developed a fine set of skills and hobbies waiting for it to be over. Over the years, I’ve learned from a lot of other folks – and even a book or two.

For whatever reason, brewing beer is a wonderfully masculine activity. This is odd, because the process is essentially the same as making soup. If you enjoy doing dishes – you’ll probably love making beer. I know lots of women who drink beer – yet few of them have shown any interest in the process by which it is created. When I find myself at a social event, sitting with a group of men that I don’t know all that well, brewing beer is one of my go-to topics to keep the conversation moving. It’s complex enough to support a deep and geeky knowledge of esoteric details – yet simple and cheap enough to allow easy access for the novice. I’ve spent many a pleasant Saturday with a couple of friends, putting a couple of batches into primary fermentation, usually with a football game playing itself out on an unwatched laptop in the corner of the kitchen.

In my early years of brewing, I would make only the most extreme recipes. I was always trying for the 12% ABV, the insanely over-hopped, or so on. These were never very good, and I found myself not able to brew more batches because all my bottles were taken up. I limit myself to six cases of bottles and a five gallon keg. That’s four batches – which is absolutely more than enough. At this point, I have a pair of recipes that I try to keep in stock for guests (and for me) – one clone of Bass Ale, malty and rich, the other an American / Indian Pale Ale – hoppy and bitter. In between, I mix up experimental batches. The current experiment is a “rauch” beer – made with smoked malt. I’ve made one of these before, and it turned out tasting strongly of bacon. While there’s nothing wrong with the taste of bacon – it’s not a good beer pairing. This new batch has turned out a lot better. I still don’t particularly *like* it, but I’m pleased that I’m able to create a beer that tastes like it’s supposed to.

Bottling is a slow and methodical process – and is a great opportunity to ruin your batch by failing to pay proper attention. Last night, I bottled a batch of the IPA in preparation for our holiday party. I found myself reminiscing on other batches, and on the ephemeral nature of craft projects. A batch of beer – even the best one ever – is still just a batch of beer. It’ll be drunk, enjoyed, and gone in time. The same is true with pickles, dried apples, and most of my other hobbies.

I find that I’m getting to be okay with impermanence these days. I find that the beer helps a little – and oddly enough, it’s more the bottling than the drinking where I find the real comfort.