27 May 2011


I said yesterday that I had gotten my genome 'partially sequenced' at 23andme.com. That is not technically accurate: I got genotyped, which is just taking one's DNA and looking at genetic variants (as opposed to sequencing the genome, which is of course far more involved, though in principle it's the same idea). As noted in an earlier post, I have also volunteered for Dr. Church's PGP (Personal Genome Project), which in fact would lead to having my genome entirely sequenced. They are looking for 100,000 total volunteers, but I think that their eyes may be bigger than their wallets on that, at least in the short term.

So why did I do the genotyping? I had a number of motivations:

1) Sheer curiosity. I just wanted to learn more about the process and its efficacy and results.

2) There was probably some morbid curiosity as well: it's not every day one gets insight into what will ultimately kill one. Of course, no one knows for sure how one will die (insert cliché about getting hit by a bus tomorrow yada yada), but genotyping can give you a pretty good picture. For the record: stroke and Alzheimer's are my two most likely means of exiting the stage. Neither came as a great surprise given family history.

3) A peek into my children's future. What I have as genetic predisposition or as recessive carrier trait can of course impact future generations. Interestingly, as far as carrier traits, I had...zilch. From Alpha-1 Antitrypsin Deficiency to Torsion Dystonia, I seem pretty much devoid of any unfortunate recessive carrier baggage.

4) Taking control of my health. Knowing that I am 25% more likely than the general population to suffer from stroke or other events or maladies stemming from atrial fibrillation, I am certainly going to be more careful about heart health. Knowing that I am twice as likely as others to develop Alzheimer's means I am certainly going to figure out a more obvious place to keep my keys. And on the other side of the coin, I am going to relax a little bit about type II diabetes: while it may be present in my family, I am far less likely than most people to develop it myself. And most interestingly, I even have some insight into the efficacy of certain drugs in the event I do fall ill. Plavix, for example, is less likely to help me should I need it, which is a very good thing to know for someone with the aforementioned predisposition towards atrial fibrillation. Knowing in advance that other alternatives might work better, could make all the difference. (On the sunnier side, should I ever need interferon, I am more likely than others to respond well to it.)

Another very useful bit of information was about diet. I am very physically active, but all my adult life I have had to work hard to keep the spare tire of 10 pounds or so off my stomach. I have usually combated this through exercise and a low-fat diet. Turns out that might not be the right approach for me; it might even be the problem. I have a gene that not only makes a low-fat diet ineffective, but actually makes things worse. With this gene, I am MORE likely to have extra pounds if I have a low-fat diet. Mind you, this isn't a licence to go and raid McDonald's every day: while I will benefit from much higher fat intake, it has to be high in just one variant of the good kind of fat, mono-unsaturated. So it's good-bye low-fat foods, hello nuts, poultry and oils like olive, canola, etc.

5) Genealogy. It confirmed what I already knew about my paternal side: Irish origins. Interestingly, on my mother's side it's a bit murkier than expected. I could be anything from Druze Muslim to Ashkenazi Jew to Basque (or something as prosaic as British origins, which is certainly the case going back the past few centuries, as my genealogical research confirms). Makes me wonder about the long path my ancestors took in their journey after Africa.

6) Getting an understanding for what I am fighting with v against. There are two possible attitudes one can take here. I can see a genetic predisposition towards not being a sprinter as an excuse not to run. Or I can take the attitude that I must try all that much harder, and note that the same trait leaves me more favorably disposed towards endurance running.

7) Having a laugh. In theory, I should more likely be a blue-eyed man of shorter than average height, with a balding head. (My eyes are hazel, I am 189cm tall and as of age 39, all the hair's still there and the shower drain is clean, knock on wood.)

All in all, I would certainly recommend the 23andme.com service. I have spent USD 99 on far stupider things. A word of warning, though: they do make you explicitly request to have certain results revealed to you, and you should consider that carefully. For example, when you log on for the first time after they finish your kit, most results are right there on the page; but for, say, Parkinson's, you have to click through a warning that basically asks, 'Are you SURE you want to know this?' It could be devastating. I was required to go through the same process for the Alzheimer's one. I opted to look because I figured it couldn't be worse than what I feared. (It wasn't. It was actually better: there's a 75% chance I will never develop it; worse odds than most people, but far better than I had feared.) But give that some careful thought before clicking through.

Beam me down, Scotty.

I said recently that there are some annoying aspects to sci-fi. But when I watch old episodes of Star Trek from the 1980s/1990s, as I did this past winter as the snow hemmed us all in, what strikes me is not how outlandish some of it is, but how much they underestimate the tide of science and technology. As I said in a recent post, there are those who suggest that we are nearing a technological singularity, a point past which society will be unrecognizable to those on this side of the singularity. I said then and repeat now that I am skeptical of this idea, but there are signs that something is hurtling towards us, for good or ill.

Look at some of the 'marvels' in those old Star Trek episodes:

-I recently saw an old episode recently in which they talked about the problem of it taking months before they could sequence a genome to find the problem at the crux of the episode. In the 24th century. In 2011, it takes a few weeks and the price is in the tens of thousands of dollars. I suspect that within a few short years, it will take days and cost hundreds. I have had mine partially sequenced for USD 99!

-In one episode, set in the future even in relation to the show's timeline, a man's sight was restored by implanting cloned eyes. A few years ago, a woman in Spain had a new windpipe implanted: it was essentially her own, as it had been 'manufactured' from an old one using her own cells.* Scientists are now experimenting with growing organs on demand. Liver failing? We'll grown you a new one and get it to you next week. That's not 24th century. That's probably a few years away.**

-In another scenario, that same blind man's clunky 'visor' was replaced with mechanical eyes a few years later. This 'breakthrough of the 24th century' is already happening now, in fact. The first primitive (60-pixel) prosthetic eyes have already been developed and approved for implantation. Wearers can at least discern light and up to eight colors, and see well enough to navigate safely. And that's version 1.0. I would be surprised if we didn't have HD-quality resolution that restored most sight within another generation or so, right here in the Dark Ages of the 21st century.

-Remember the old tricorders and communicators from the original show? My iPhone can do 1000 times more than those clunky things ever could.*** I can whip out this USD 199 device and do things Captain Picard would need his ship's computer to do.

-Speaking of computers. Are you kidding me? That piece of junk on the Enterprise often did things in hours that my laptop could do in minutes or even seconds. There are already supercomputers capable of memory and speed that are comparable to those of a human brain. In ten years, we'll probably have laptops of that capacity. And how about those huge computers on the original series?! Please. We surpassed those before Shatner bought his third toupee.

-On a related note, I saw an episode in which the characters were in awe of an android that performed at 60 teraflops. I am no expert on this, but from my admittedly cursory investigation, it seems that's peanuts! Our current supercomputers are measuring in petaflops, not teraflops.

So skip the beam-up, Scotty. I am doing just fine down here.


*You know who you are when I say that at least this time I remember where I read it.

**Well, assuming they can sort out the pesky issue with the connections: making an organ and hooking it up to the body's blood supply are two separate tasks, and it turns out the latter is harder. It's like being told that creating an HD TV from scratch is easy-peasy, but figuring out how to plug it in is superlatively difficult.

***Except getting me beamed up.