I haven’t whined much about the shoulder lately, because there hasn’t been much to say. Every day it hurts a little less, and every day I surprise myself by using it to lift something slightly heavier than the day before. On the other hand, every day I also surprise myself by moving it in some way that causes not very much pain, but enough to make me instantly back off and change my approach.

Yesterday, I had my physical therapy assessment. Turns out that the therapist is an old buddy of my judo coach, and another of the guys from the judo club has a brother who owns the sports therapy clinic. Small world. Anyway, this guy actually *did* judo for many years. He also struck me immediately as both smart and competent. He looked at me, moved my arm around, and generally touched and examined me.

Apparently the surgery to repair this is big and nasty. A large incision along the top of the shoulder, and then lots of clamps and wires to hold the bone back in place. It’s very invasive and only works some of the time. The reasons one would do this are an inability to work, or cosmetic. I looked at the guy and said that my career as a male model wasn’t going anywhere anyway. He seemed to like that.

Given that I’m okay with a lump, I should be back to full strength in a couple more weeks. Full strength, of course, is a modified concept. I won’t be doing the throwing part of judo anymore. That shoulder is never really going to be the same … and hitting it again in the same way would be a Really Bad Idea. Still, for grappling, striking, and generally moving around I should be fine.

Today we started the PT part of physical therapy. This involved a pair of electrodes on my shoulder for the “electro-stim,” to get things moving, thing some light resistance range of motion stuff, and finally a nice soft-tissue massage of the shoulder. It wasn’t nearly as painful as I had been told to expect.

Check out my quad architecture binary:

sh-3.2# file common/bin/dsh
common/bin/dsh: Mach-O universal binary with 4 architectures
common/bin/dsh (for architecture ppc7400): Mach-O executable ppc
common/bin/dsh (for architecture i386): Mach-O executable i386
common/bin/dsh (for architecture ppc64): Mach-O 64-bit executable ppc64
common/bin/dsh (for architecture x86_64): Mach-O 64-bit executable x86_64

And I only had to learn about the --disable-dependency-tracking flag to do it! Yeah, what’s the worst that could happen when you pass an argument to autoconf and thence to make telling them to not manage your dependencies.

Dear Apple: In terms of ease of use … why do I need to know this crap in order to make a binary that will work on all your recent architectures?

I spoke at the Bio-IT World Expo last week. It was pretty good. The conference was much larger than last year. As usual, it struggles between being a trade show with vendor talks and an academic forum. Personally, I like the struggle. If it were pure academic, I wouldn’t fit in very well … and if it were pure trade show I wouldn’t go to the sessions. Marketing gives me a near allergic reaction.

Slides are here, if you’re curious, plus a picture of me looking tired. You can’t even see the lump, so maybe it’s just that I *feel* like freakin’ Quasimodo.

As I’ve gushed in person to several folks, the closing keynote by the CEO of 23andme was a particular highlight, since I’ve bought their product. It was interesting to see that their long-range plans include both social and scientific goals.

The closing panel was fascinating to me. It was very much a selection of archetypes:

* Two genomics company CEOs (23andme and Navigenics)
* George Church, the Harvard professor who invented the chemistry behind next-gen DNA sequencing.
* The editor in chief of the New England Journal of Medicine, who has famously been quoted as saying that if you have a spare $1000 to spend on your health, a gym membership would be a smarter buy than a SNP analysis
* Two technophiles, including the CIO of Harvard.

Like the total fanboy I am, I sat in the front row next to cariaso of SNPedia, and giggled when he got a nod from the podium during the keynote.

Other than that, I won’t try to capture the whole conference. It *did* include one overly gluttonous corporate dinner, as well as a few good introductions.

One of the scientists that I’ve worked with for a few years just got elected to the National Academy of Sciences.

I think that’s pretty sweet.

Also, jwz just summed up in a sentence my core point in many, many technical arguments:

Excuses for why you think it’s reasonable for it to work worse don’t make it work better.

Just to get this out of the way: 23andme. There. Google has been fed Welcome, news-hungry bloggers with constantly running searches.

I finally got my data yesterday, a full 11 weeks after my tube of spit was received. My whining was noticed, and eventually there was some explanation on the company blog. In response, there was sympathetic commentary as well as some outright snarkiness in response. Sheesh, Sherpa. We all know you’re smart. Relax.

In any event, I say “whatever.” Business is hard. I’ve finally got my data. Let’s play.

I deliberately held off on judging the web interface until now. Their example genotypes are loaded with somewhat interesting stuff. How would it look on data from an average height, average build, no major complaints white guy? My first thought was that 23 and me has done a remarkable amount of work to make the basic biology comprehensible to the interested layperson. I have no idea whether Decodeme and Navigenics have done similar flash and java whizziness. Perhaps unfortunately for me, I’ve had a bunch of biology classes and have been doing bioinformatics for a living for more than a couple of years. Their tutorials are old hat, and while the miraculous wonder of DNA replication is still pretty newsworthy, but that’s not why I bought a ticket for this particuar ride.

If you don’t already know how DNA, SNPs, and Microarrays work, it’s a good intro.

My first impression of looking at the Gene Journal was “this is it?” I knew up front that we know next to nothing about how these data points relate to physical predispositions, aptitudes, and diseases. Still, I was bummed when I saw only 58 entries in the gene journal. These are the detailed, annotated pages that 23 and me provides about specific physical conditions. I did get a snicker out of the fact that one of the subsections of the journal is named nether regions.

Since I was already giggling, I dug into the Prostate Cancer page, and saw sort of what I was expecting to see. A nice little write up on what prostate cancer is and what it does, and then a couple of charts comparing my relevant SNP with the population baselines. They even do a slick little thing with the set of five markers that are currently implicated in this condition.

As I clicked through, the data was absolutely inconclusive … as expected. A percent higher here, a percent lower there. The very best research that they cite has at least two studies, each of which has at least 1,000 participants. That seems large until you start dealing in fractional percentages, at which point you’ve got barely enough data to say anything at all.

Next, I noticed what was missing. The stone cold indicators currently used in genetic testing for Alzheimer’s, Huntington’s, and so on are simply not present in the gene journal. The Breast Cancer indicators are in there, but there are only two of them. Contrast with the SNPedia entry where an ungodly list is present.

SNPedia is run by my friend and colleague cariaso. The vast majority of annotations in there are the product of his evenings and weekends. Let me say that again: One or two people, in the evenings, have presented a far more comprehensive resource than a team of venture capital funded biologists. Now, the SNPedia AJAX and java whizziness is not nearly on par with 23 and me, but that’s not what I’m here for.

To continue, cariaso has put forward links from SNPedia into 23 and me’s page. I can very easily take some genes that are implicated according to SNPedia, go into my raw data from 23 and me, and bounce back to see what that genotype might mean. In fact, I can do the math that 23 and me might have done and calculate a more comprehensive set of odds than they did. Turns out I’m at a slightly elevated risk for breast cancer. I’m also a guy. Take that statistics!

Back to Alzheimer’s. That’s also a simple one. I’ve got the “less likely to get Alzheimer’s” version of APoE. However, it took a good 10 minutes of clicking back and forth between the two sites. The 23 and me page about APOE tells me less than nothing. Further, there isn’t even a gene journal entry for this largely genetically determined and very well researched disease.

I can see a reason for this: If I was in the business of selling genotyping, I would have nightmares about the first time a customer killed himself when he learned about some propensity or condition. The same sort of standards that apply to revealing HIV test results might well apply here. As a society and as individuals we will need to spend some hard time thinking about how much we want to know and when we want to know it.

So they’ve deliberately (it seems) scrubbed the gene journal of easy and clear evidence for simply diagnosable risk factors. Thanks guys. I can download the raw data and do the work myself … but a summary page eludes me. That’s the useful stuff that I was looking for. I know that I have a “58% chance” of having brown eyes, and that my earwax is wet. Further, I knew that my dad’s fathers came from Ireland, and that I’m Northern European on both sides.

Me? I want to know it all, and I want to know it now. Therefore, I downloaded my data into a 4.5MB text file. First look:


Total Lines: 576119
Comments: 14 lines
SNP data points: 576105
Uncalled (--): 3189 (0.5%)

So that seems fair to me. Half a percent “no call” rate is actually pretty darn good. Note that this says nothing about error rate, nor about quality of the called SNPs. It does say a bit about where they set their quality thresholds. I’ll dig into that on a second look.

Then I used my colleague cariaso‘s Promethease to churn through an analysis. This is a program that does exactly what I was doing by hand. For each data point, dig into SNPedia, figure out whether it’s associated with any diseases, and if I have the rare version. Then it produces a report listing my information both by disease and by rarity. That’s what I was looking for. He and I had a nice chat about usage, being trapped on Windows, and about data privacy.

Even with my shiny promethease report, there’s still not much information in there. The state of human genetics is “just getting started.” However, I plan to run Promethease once a month or so as a way to keep up on the advances in science relevant to me. Hopefully in a few years there will be more to read about.

I picked up A Fighter’s Heart by Sam Sheridan at the airport on the way back from VA. I’m nearly through it already, a quick and easy read.

Sheridan has fought in several different styles over the last decade or so. He attaches himself to an intensive gym in Muay Thai, MMA, Jiu-Jitsu, Boxing, or whatever … trains for three to six months … and then tries to convince his trainer to find him a money fight at the appropriate level. He funds this habit by writing for the Men’s Journal, Sports Illustrated, and so on. It’s sort of a one-man Human Weapon.

I like his writing style, as well as his stated reasons for stepping into the ring again and again. A few of his off-the-cuff comments are totally dead on with my experiences to date. One that I keep coming back to is his description of grappling, the “ground game:”

There is nothing so frightening as being on the ground with a guy who really knows what he’s doing; it’s like being in the water with a shark. You’re struggling, desperate, trying to escape, and suddenly you can’t breathe, you’re smothered, and you can’t see, your arms are getting twisted off, and you “tap” and then it’s all over.

That, broadly speaking, has been my experience rolling with any of the skilled guys at the judo school.

A friend asked my opinion on forgiveness. My answer was long and sufficiently general that I figure I’ll share it here:

I very much feel that some kind of contrition has to occur for there to be forgiveness. I don’t buy into the Christian form which is, by my understanding, saying that it’s ok the person (who needs to be forgiven) totally screwed you over and that the mean or bad or evil action doesn’t matter anymore.

I just sent a tube of spit to 23 and me.

23 and me are one of three companies already up and running with “personal genomics,” and I’m getting what passes for a thousand bucks worth of my genome analyzed. You give them a credit card number, they send a sample collection kit, and in short order you log into their web site to see the results of their analysis. Hopefully, they won’t have broken the “download your raw data” feature before I get access. While their web portal is interesting, the potential to use my own data directly is way, way better.

They use a machine from a company named Illumina. The experiment provides a “read” on both strands of my DNA for a single letter at each of more than 600,000 locations in my DNA. These are locations where we have some sort of evidence that a “single nucleotide polymorphism” (SNP) occurs. That is, a one-letter swap that somehow matters in genetics. SNPs are one of the things that count as “genes” these days.

For some of these locations, we have pretty good data on physical traits that are correlated with specific letters. Here is an example entry in snpedia called “Rs1815739”. In this case, the evidence suggests that there is a correlation between particular letter pairs (CC, CT, TT) and whether you’ll be a better “sprint” or endurance athlete.

For the vast majority of the locations, we know next to nothing. They’ve been identified as variable locations … but nobody has a clue what affect (if any) they have. By “vast majority,” I mean “more than 99%”. Seriously, I’m getting data about myself that will be unwrapped … project by painstaking project … over the next couple of hundred years. I plan to crib a couple of scripts from cariaso to email me research summaries of my loci of interest every morning.

For the record, there are a bunch of other things that also count as “genes” which are not measured by this experiment. This is the one that happens to be really easy to measure in bulk right now.

The consent letter in the package is telling:

You should not assume that any information we may be able to provide to you, whether now or as genetic research advances, will be welcome or positive.

So there we go. I’m “getting my genome done,” for a few reasons. Primary among them is that I find myself in the role of explaining this technology to friends, family, and customers. If I’m going to form some sort of opinion on it, I’d better be well informed about the whole process. I also have some simple curiosity about the basics of my genetic makeup … and there are a few “gotchas” out there that would let me adjust my lifestyle in my early thirties to increase the odds of living into my late 90s.

So how does it feel? It feels a bit scary, actually. I wasn’t expecting the degree of approach-avoidance that I felt, looking at that little plastic tube … and then looking at the fedex envelope to ship it off. I know better than most people that “genetics is not destiny,” … and I’ve been saying for a long time that more accurate information *always* leads to superior decision making. Still … do I really want to know about Hodgkin’s?

Yes. Yes I do.

It’s time to iterate on the year in review traditions. I’m open to any and all of these … and I expect that I’ll do a bunch of them. This one is the “copy and paste the first sentence that you posted in each month of the year in question.” Here are results for:

2004
2005
2006

Aaaaaaaand, here’s 2007. I’m tweaking the rules to allow more than one sentence, up to a paragraph:

Jan: After all the adventures, we’re finally home. I’m exhausted, and looking forward to the solace of an ordinary work week. Was great to see the entire family.

Feb: I’m on a mass mailing list for NASA folks, through the consulting work I’ve done down there. Just got an interesting email:

Mar: Man, I answer a couple of support questions and all of a sudden they’re all like “OMFG, you’re really, really answering mail right now! We have a bunch of totally new feature requests that we’re going to phrase as bug reports in the hope that you’ll spend the whole day rewriting major portions of your code to address them! Please please please please please?”

Apr: I have finished both God of War, and God of War 2. They are amazing games … pinnacles of the 3rd person single player genre.

May: I gave my talk yesterday at Bio-IT World and it went okay.

June: Posting from the Hospice St. Joseph in Port Au Prince, Haiti.

July: I got home from Atlanta between 2 and 3am on Friday morning. On Friday at 7pm, I flew to Detroit to see both sides of the fam. I am now delayed in Baltimore, awaiting my flight back to Providence. Tomorrow morning, I shall rise at beastly:30 to go into Boston and work for MIT, integrating new machines into an existing cluster for a rockin’ cool customer.

Aug: I want more time.

Sep: Excellent weekend with the fam, down in VA.

Oct: The die is cast. We have keys to the apartment. The cats are ensconced, and pissed off.

Nov: We had technolope and capital_l over for indian food last night. We opened up a 25 year old bottle of Blue Nun Riesling that they had found … and it was … different.

Dec: Tomorrow … who knows?

Went to a meeting of the greythumb group this evening. Cool stuff. Smart people, in many different ways. This month’s speaker talked about synthetic biology and designing organisms from scratch. I’m next month’s speaker.

Among the other people there, I met Virgil, the guy who made the Wikipedia de-referencer. He was mentioned on The Colbert Report … from which I recognized him. Odd and interesting. I thanked him for sticking it to the man.

After that, I went across the street with technolope to another bar for another bit of socializing. Wound up staying and talking far too late about plans to find and mass-moon the google camera truck … and fantasizing about a mighty artistic commune in Detroit … in a 16,000 square foot mansion that’s currently listed for sale at less than a million bucks.

My life is awesome.