30 June 2004



I spent last night taking shots of Goldschlager and Jaegermeister while watching the Red Sox roll over for the Yankees. I also threw my baseball hat at the TV several times and threatened various household objects with a baseball bat until I wisely relinquished same to Amrys's protective custody.

I don't know what I'm going to do if they lose again tonight. Maybe I'll become a Phillies fan.

This one's for you, MRhé

There's an excellent Kristof Op-Ed piece in today's Times. The thing I fear most about the future of America is the increasing tendency to replace rational argument with vitriol and understanding with zealotry. Our political culture is becoming defined by how fanatically we can devote ourselves to The Cause, regardless of what that belief actually is.

29 June 2004

Ah! There is a point to all this.

Despite being a Monday, today was a productive day at the office. I did a fair bit of useful coding, ran some analyses for the Pinnacle Diabetes Project and tracked down the 2nd HapMap QC dataset to start cooking it up as a side project.

But what was even better than that was the discussion I had with Mark while walking over to the Genome Center for the weekly HapMap meeting.

Whenever I get feeling run-down and useless at work it always helps to talk to Mark or David, because they're both excellent at grasping the big picture. I guess that's what makes you a success in upper-academia.

Anyway, this particular discussion was mostly about the loose ends I need to tie up before leaving Broad for Oxford in the fall. I need to make the documentation for Haploview way more self-sufficient, especially if Bioinformatics accepts my Application Note about same. Plus this is possibly my last chance to do a large update, which means fixing several bugs, patching what I'm 80% sure is a memory leak and adding one or two new features. Beyond that I've got more work to do for Pinnacle, some additional HapMap work before the next big meeting in September and coauthoring the ENCODE analysis paper. Finally, the most exciting summer goal is to start reading up on some of the work my future labmates are doing and dive into some hard-core statistics studying so I'll be ready to go at Oxford.

The bottom line (for those of you still reading) is that the conversation made me feel like there was a point to my work and helped to motivate me to push hard in the next few months in preparation for my big leap across the pond.

24 June 2004

We Sucked


I was just randomly browsing the 2004 Mystery Hunt pages and I came to a not-too-surprising conclusion: we sucked.

So many of those puzzles were so horrendously broken it isn't even funny. Looking back on it, I totally misdirected my efforts. I was so caught up in planning the overall theme and sticking my nose in the organizational business that I totally missed the fact the the puzzles totally blew.

I just clicked through a bunch of puzzles, a few of which I had never even seen, let alone tried to solve. The recurring theme with them is a solid idea for a fun puzzle ruined by miserable execution. There were puzzles that had illogical steps, puzzles that involved overly complicated mechanisms and puzzles that simply weren't revised carefully enough. The excuse I've heard bandied about is that most of us were puzzle-writing novices, which is true, but I think it speaks more to our terribly broken testing procedure.

There were a number of ways in which we weren't testing puzzles very well:

  1. Many puzzles were literally solved over a period of weeks and thus declared "good 'nuff" because at least it was possible to figure it out. This is a totally inappropriate metric for a puzzle designed to fit into a one-weekend competition along with 100+ other puzzles.

  2. Somewhere along the line a few of the most involved people totally lost touch with the reality of whether a puzzle is easy or hard. This resulted in several puzzles being deemed "way too easy" and as a result being made impossibly hard.

  3. Tons of puzzles just "fell through the cracks." Somebody got a hint to overcome some really horrendous logical gap and it just never got patched. They made it to production day still lacking a clear path from one step to the next.

And now I feel worse than ever about my own failings. I was always focused on the wrong things and I simply didn't do enough puzzle writing or puzzle solving to really be as useful as I should've. Next time I'm on a winning team I'll do better.

P.S. Bonus points to anyone who knows why the picture is especially appropriate.

All the Lefties in the House Say HEYYYYY

Ahhhhhh. The sweet, sweet relief of someone who can express my feelings eloquently, thereby eliminating the need for me to babble.

[Courtesy of the Good Doc]

Spreading Democracy

I've been thumbing through a few chapters of John W. Dower's Pulitzer Prize winning, Embracing Defeat: Japan in the Wake of World War II recently. It got me off to thinking about America's adventures in nation building in the last 60 years, from the nearly unmitigated success in Japan to the current muddle in Iraq. In both cases the Americans tried to give a Constitutional democracy to a people for whom the idea was very foreign. The difference between this approach and our own Independence movement is, of course, that we demanded a government of the people, by the people and for the people.

Now, the postwar Japan and Iraq situations are wildly different, but there are some interesting parallels. In both cases we won the war and were left holding the proverbial bag of occupation. The Japanese weren't so intent on killing us and those in their own country who supported us as some Iraqis are, but in both cases our goal was the same: take a system of national polity which we found unbecoming to a modern nation and replace it with a Constitutional democracy which will uphold personal freedoms and the concept of popular sovreignity.

My first obvious question is, "Can this ever work?" Is it possible for a foreign power to impose its own view of the world on a country and expect it to take hold? Don't get me wrong, I'm not dabbling in PC-nonsense here: I firmly believe our (the free, Western world) system is better than most, but it seems very tricky to get it to work unless the actual people in question are pulling for it. In the end, the Japanese managed to take MacArthur's Constitution and make it their own. They wanted it badly enough to keep on trying after the occupiers went home. Do the Iraqis? I don't know. And it certainly doesn't help that terrorists are blowing up police stations across the country while they're taking their first stumbles toward electoral politics.

22 June 2004

Movin' on up

Well, it seems fairly certain that I'll be leaving fair Cambridge this fall to enroll as a D.Phil. (the haughty Oxford term for a PhD) student in the Bioinformatics Group at the Wellcome Trust Center for Human Genetics at Oxford. Tentative start dates are either October 1 or December 1, pending various administrative negotiations relating to my funding.

So that's something, I guess.

17 June 2004

I'm Awesome

I was ambling about the office (which I tend to do) talking to Claire and I started fiddling with crap on the desk in order to keep my hands busy (which I tend to do). It was a few moments too late when I realized that my latest idle motion was to frob the switchhook of the desk phone which Kirby was speaking on.


Today is a good day.

I presented some data from the Human HapMap Project to the Broad Institute Medical & Population Genetics group. It's what's sometimes called a "supergroup" meeting where lots of lab groups come together (in this case once a week) and present recent work on a rotating schedule. This week was the Broad HapMap group, and I was tapped (along with 2 others) to talk for 15 minutes. It was a good intermediate step between presenting to a group of people you know really well and presenting to complete strangers. I knew most of the 50 or so people in the room, but there were some I didn't, and there's definitely a good sprinkling of hard-assed PI's to ask obnoxious questions. So like I said, good practice. The talk went just fine and now it's over, so I can get drunk. Well maybe not quite yet.

The other big work-news of the day is that I'm finally submitting my first first-author paper. It's to a smaller, specialty journal, but it is a big deal to get your very first bit of work published that you can really call your own. I'm pretty psyched about it, especially because Mark has been dragging his feet on this for a while (not because he hates me—just because he's supernaturally busy).

15 June 2004

Sea Story

This still cracks me up, 7 years removed. And gawd, some people have mouths like sailors.


No, I'm not talking about Goose, I'm talking about the amazing Coors Light commercial. The Silver Bullet has far and away been leading the pack of beer advertising lately. Wingman is a true classic, but the recent "Man on the Silver Mountain" series has been quality also.

For those of you who want to perform your own wingman tribute, check this skrit out.

Two more comments before I shut up:

  1. The one flaw in that wingman ad is that the shackling girl is pretty good looking. I realize the implication is that she's a hose beast, but imagine the following scene: You're hanging out in a bar with music so loud that you can't hear what this girl is saying and you're totally bombed. Are you really going to care that she's annoying as hell? Why not just check her the funk out?

  2. Googling for coors wingman returns almost entirely bløgs. This really is becoming a huge factor in interwang content, and I stand by my previous assertions that the bløgosphere is replacing the personal web page as the common man's gate to the world of online.


During one of my standard interwang browsing sessions at the office I stumbled across this essay by Paul Graham about nerds and the American secondary school system. I think he has a lot of interesting observations, although I think he extrapolates too far in his "secondary schools are little more than prisons" arguments. My favorite quotation:

There was something else I wanted more [than to be popular]: to be smart. Not simply to do well in school, though that counted for something, but to design beautiful rockets, or to write well, or to understand how to program computers. In general, to make great things.

This is, I think, what makes MIT such a wonderful place; it's full of people who want to make great things. That's why the Arts really flourish at MIT too, despite what nearly everyone expects—the same people who want to build rocket engines also want to write poetry.

11 June 2004

Paul Krugman is a Jackass

Krugman published his second whiny, Reagan-bashing Op-Ed piece in the Times today. He succeeds only in being petulant (which is his forté anyway).

"Hey, hey, wait, stop watching that funeral, listen to me, Reagan wasn't as good as people say! Wait, lemme tell you about all the great things that Bill Clinton did. Reagan was a sucker."

The man is being buried today. I'm disgusted.

Not that I'm advocating the cloying coverage provided by some of the cable news networks. For my money, C-SPAN has the right idea here, as per usual: broadcast footage of the various rites without any commentary.

10 June 2004

What if we had 12 fingers?

This post is high-nerd-content. Consider yourself warned.

I was thinking today about how we live in a joint binary/decimal world. It manifests itself in all sorts of ways that are easily overlooked. Take, for example, the fact that a 25th anniversary is often made into a big deal. Why 25? It isn't a product of 10, which is usually the period over which annual events are especially commemorated (c.f. last weekend's 60th anniversary of D-Day). 25 is special, of course, because it is the quotient of 10 squared divided by 2 squared. It arises from combining our two favorite counting systems.

As Scott will tell you, there's a long-standing fight in this country between the older base-2 measurement system and the base-10 metric system.

08 June 2004

The Gipper

Certain events (e.g. the death of a former U.S. President) tend suddenly to pop up in bløgs all over the place. Everyone wants to weigh in — be it on politics, thoughts on Alzheimer's, the media coverage, whatever. Bløgs are like editorial pages that way: diverting in uniform from the writer's usual hobby-horse to say a few words on some recent topic of great import. My reaction to Reagan's death is muted. I was too young to have strongly felt political feelings when he was in office. My first real political memories were around the time the Berlin wall fell, and I don't have a sense for what it was like living in Cold War America.

What I don't like is how this has provided an opportunity for people all over to make ill-informed and overly-generalized statements about the years from 1980-1988. People like to talk about either how wonderful or how horrible Reagan's years in office were. Like everything else, the truth lies in the middle somewhere, but that's not even the point. For one thing, when a statesman dies it is appropriate that we should pause from our daily lives and remember all the best things about him as a President and as a man. It is wholly appropriate that we should treat him with a certain reverence and dignity in these days after his death. You don't have to love him or agree with how he governed, but I believe that the time to express your dissent is not while his coffin lies in the Capitol rotunda.

And even if people want to talk about the victories or failings of his political career, do it with some logic and factual basis. Some bløg entries and comments I saw were so wildly inaccurate and partisan that it made me ill. And that brings me back to what I hate about American politics in general: the extreme polarity of the system. Nobody admits his ideological opponent might possibly have some insight to offer; instead of forming affiliations based on our beliefs we let our beliefs be dictated by The Party. Instead of trying to truly serve this country, our supposedly honest, trusted leaders tell us bald-faced lies to get re-elected.

Enough of that. Let's observe a moment of silence for the Gipper.

Page 23

So I've seen this pop up on bløgs every so often, most recently at ergodicity.net So I picked up the nearest book, turned to page 23 and read the 5th sentence in order to forecast my future:

"Unfortunately, this often produces instant "experts", full of confidence and naiveté but with little experience in building real, production-quality applications."

04 June 2004


I saw a squirrel get hit by a car while walking home from work yesterday.

I had always assumed that squirrels, pigeons and other urban creatures had adapted to their surroundings to the point where they could thrive among people and concrete. Apparently this is a misguided assumption. The squirrel ran down a tree in front of me, zipped across the sidewalk and ran straight into the street. The approaching car wasn't moving that fast and was on the far side of the street. The squirrel ran straight onto the street and must've seen the car, but instead of stopping or turning he just gunned it straight ahead: under the car and clipped by the front driver's side wheel.

After the car went by I saw the squirrel lying motionless on the road. Then he convulsed. Then he was still. Then he started twitching again and finally started doing backflips and somersaults 3 feet in the air. His body was just flailing the muscles wildly. It was pretty awful and I wished I could put him out of his misery, but there wasn't much I could do. So I went home.

02 June 2004

Opening Move

File under "Lines to Open a Short Story":

"I look forward to once again living in a place where the cars have rear seat belts."

Ganked from Enrico Steelazzo

Ken Burns

A much better commencement address than James Wolfensohn gave in 2002 in Killian, courtesy of Dale.

01 June 2004


Only in programming books do you have to turn past 4 pages in the index before getting to the letter "A".

Motivational Speaker

As in, I need one. Work lately has slipped into that phase where I sit around looking for something to do other than work. Which is not that sweet a place to be. So it's time to cinch the belt a notch and dive back into it. I mean, hell, at least there's something interesting lurking at the bottom of my list of mundane tasks. Why hold back from the process of discovery?

Time to get the machinery of the mind churning again. One foot in front of the other...