Tuesday, September 9, 2008

Genome or Playstation? Hmmm...

Well, we're still here, so the LHC hasn't destroyed the universe... yet. Good news.

Recently there was some not so good news for people who deposited their genetic information (not that way!) into public databases - there is some concern that this information can be tracked back to individuals. This doesn't seem like such a big deal, and it won't be until one day we apply for life insurance and they tell us, "Well, we found your genome online and it looks like you have a 10-fold elevation in your risk for contracting the hoobajabbies within the next 11.6 years, so we're going to need to increase your premiums." Seems a little science-fiction and Big Brother, until you find out that 23andMe (who I've talked about before) can now "sequence your genome" for the same price as a Playstation 3.

Now, I say sequence in quotation marks because they don't really sequence the whole thing, which so far only Craig Venter can really do, at the cost of tens of millions of US dollars. Before the currency started plummeting. Only two people have a data file containing their whole genomes at this point, and they are Dr. Venter and James Watson, and even what they have is a "best guess" from a computer-guided reassembly of their whole genomes from sequenced fragments.

The As, Cs, Ts, and Gs that make up your DNA are known as nucleotides, and there known places where there are differences in the population. These are known as single nucleotide polymorphisms (SNPs), and we have discovered thousands of them. Some of them are even associated with certain (real) diseases, although these studies represent correlations rather than causes. Still, insurance companies calculate premiums based on actuarial tables - statistical correlations - and I don't want them exploiting a $400 sequencing service to make a couple bucks by nailing people who happen to be born with a couple bad nucleotides.

I am seriously impressed that our legislators have already been thinking about this, but clicking on the government link for information about genetic discrimination legislation gets 404'd, which leads me to be believe that it's not exactly a hot issue these days. Like puffin poop.

Sunday, September 7, 2008

The End of the World?

The Large Hadron Collider comes online Monday and starts doing weird things that the universe hasn't seen happen to its particles since around the Big Bang, apparently. For an easy-to-follow lay explanation, see this link, which beats the hell out of the biology songs cropping up on YouTube. Some are arguing that this thing could end our world by creating black holes on the planetary surface, but I feel that if black holes were that easy to make, we'd have them in our backyards. Or maybe that's where lost dryer socks really go.

In a similar vein, it's also the end of the longest minority government ever in Canadian history, as Stephen Harper asked Michaelle Jean to dissolve the Parliament this morning. We'll head to the polls for another election on the 14th of October - the 3rd time in 11 years - and we'll end up with another Conservative minority. Harper's strategy must have something to do with massive turkey consumption influencing voter choices, as last time we had elections just after Christmas.

This blog will get hijacked by incredibly amusing (and potentially vindictive and offensive) political tales every once in a while, because election time is my favourite. We'll start by ripping into David Emerson, the shifty representative from Vancouver who crossed the floor 2 weeks after being re-elected as a Liberal in his traditionally left-wing riding. His quotes in the CBC's article are gold - "I was never a Liberal," he says, seemingly forgetting the years 2004-2006 and missing the signs festooned around his riding during both those elections proclaiming him as a Liberal candidate. "I think I had a good shot at winning [this election]," he speculated, although a Conservative hasn't been elected in that riding since 1958, and his own Conservative opponent in 2006 finished 7, 000 votes behind the 2nd-place NPD candidate.

A particularly astute commenter on the CBC site theorizes that, although Emerson says he's leaving politics because of the commute from Vancouver to Ottawa, Harper will appoint Emerson to the Senate and his Cabinet, much like he did with Michael Fortier in 2006. Although I'm not sure that he'll end up as a Minster again, I think Harper will push Senate reform to the back-burner of this election campaign, and there will be another Senate appointment when he wins another minority. After all, it's not like Emerson would even have to show up for that job...


I don't have a lot to say on science today, although it was kind of gratifying to see an entire issue of Nature devoted to "Big Data" and its impact on science, which I touched on months ago. More on this to come later in the week, with incisive political commentary on the mousiness of Stephane Dion.

Another interesting tidbit - a huge ice shelf has broken free of our very own Ellesmere Island (the big one in the Arctic beside Greenland). This is not only just a sign of global warming and the problems we can expect, but also a none-too-subtle reminder that the fabled Northwest Passage will soon be open for business. We don't tend to think that much about borders in this country, but we definitely have them, and there is definitely territory under dispute in the Arctic between ourselves and the USA, Russia, and Denmark. Most of these disputed borders are in areas close to the Northwest Passage, and will become the subject of heated diplomacy between our countries as the prospect of profiting from goods shipped through this nautical shortcut to the Panama Canal becomes a reality.

Tuesday, September 2, 2008

We are nihilists, Lebowski! We care for nothing!

I commented a while ago on something that Dean Ornish calls genetic nihilism, a great turn of phrase that I will deftly procure for myself. This is a sort of view in which we say "well, my DNA has already programmed my health and/or behaviour, whether I will get diabetes or cancer or an aneurysm while doing backstroke in the community pool." Which, in addition to being untrue, is a pretty irresponsible way to live.

I thought of it because of a Swedish study showing that the presence of a certain variant of a gene in males is associated with increased prevalence of "marital crisis" in the last 12 months, reduced proportions in number of men married, and lower scores on a sort of "pair-bonding index." And the headlines were awesome - "Why men cheat" (Science Magazine), or "Commitment phobes can blame genes" (BBC). These are great examples of genetic nihilism. We are expected to take it at face value that men fear commitment and cheat on their wives and girlfriends, and furthermore that these are parts of being male programmed into DNA as much as a penis is, so we should be able to find a gene that makes it so.

No one is ever going to find that gene, because it doesn't exist (along with the "penis gene"). The authors of this study do some fancy calculations and say that about 28% of the variation they saw in the study were inheritable from their parents. Now, I'm going to say that heritability is not just a question of genes being passed down, and if you want to argue about that let me know. The rest is from "environmental factors," which is to say everything other than your parents.

We have roughly 25 000 protein-coding genes in our cells. Let's say 1% are involved in mating behaviour, which is probably a ridiculous underestimate given the importance of mating to continuing the species. That's 250 genes involved in mating behaviours, which are only the genetic part of their heritability measure, which in turn only accounted for about 28% of the variation in the study. While some of these genes might be more important than others, the assertion that a different version of a single gene will double your chances of being unmarried or in a turbulent relationship seems unlikely at best.

This study does have an interesting design, however, involving some 500 same-sex twins both married and unmarried. I hope they run some fishing trips (technical term: gene microarray) looking at polymorphisms on other genes that might be related.