Monday, January 13, 2014

How numbers behave

We have a water cooler at work, with those big water jug things. When you go to get some water and the jug is empty, you have to replace it; this probably happens 2-3 times/week.

I encountered an end of a jug (and therefore replaced it) three times in my first two weeks in the lab, and then I didn't encounter one again until this morning, nearly a year later. My brain immediately started trying to read meaning into this. Why then? Why now? Why not all the time in between?

The reason, of course, is "just because". If I ever create a course called "Psychology and Statistics" (spoiler: I won't) you can be sure there will be a segment on water coolers.

Saturday, January 11, 2014

Running downhill

I'm going back to grad school this year. It's been a long time coming -- holy hell, I'm 36; I have articles of clothing that are almost as old as most of my classmates will be. I've been working in computational biology for 8 years, now, since I left the software industry. Over that time I slowly came to the realization that this is really what I want to do with my whole career, and that I really needed to invest the years to get a PhD in order to do it at the level I want to. So far, without a PhD, I've pieced together a couple of really great jobs doing some really fun work, but that's all been a matter of luck; to make this into a lasting career, I need to do what everyone else around me did in their 20s.

I need to go back to school, both to get the credential I need to be taken seriously and to get the knowledge I need to do those jobs as well as I can. Even when I come out on the other side, I'll be the low man on the totem pole; it'll be a big step back in many ways. I may never make as much money again as I do now; if I do, it'll be a long while. But that's OK, because I'll be much better at what I'm doing with my life than I am now. Different doors will be open to me.


That's the story I tell most people about why I'm going back to school. It's pretty true, actually, and if it weren't pretty true I wouldn't be doing it. There's another part, though. The other part has repeated itself dozens of times during the last 8 years, and it goes something like this:

We all went to the bar this afternoon, in my lab. We call this "running downhill". That's hilarious, because my boss always talks about how we take the quickest path to getting drugs into the clinic, and he calls that "running downhill", but there's also literally a bar downhill from us. We don't actually run there; that would be too much effort.

Anyway, we all went to this bar, and while we were there, a colleague of mine who had a couple drinks in him made a comment about how, when they replace me after I go to grad school, maybe my replacement can "do some science, too".

He might have been kidding. He kind of acted like he was kidding. If he was, he was kidding because there's some truth there, too, at least in the collective mind of my chosen field. It doesn't matter how important my work is or how many publications I have. I don't have a PhD, so what I'm doing isn't science. It's just a matter of definitions. It probably doesn't help that I'm currently a computational researcher surrounded by wet lab folks, but I got the same kind of comments when my colleagues were computational.

I used to hate this phenomenon; it cut me deeply, over and over, and frankly it's the thing that got into my bones and made me decide to go back to school.

But now that I'm headed back to school, I love stuff like that. It shores up my resolve to go back, which is something that weakens whenever I actually stop to think about the craziness I'm about to embark on. That comment right there, by my coworker at the bar, was me passing my qualifying exam. Or maybe it was a dozen pages of my dissertation. Or maybe it was me powering through a week of late nights in the lab. Because every time a coworker with a PhD makes a comment like that, I store it up. It's like a giant fucking battery, and it's been charging up for most of a decade now. I'm going to need a lot of damn energy from that battery to get through the next five or so years, so I'm especially grateful when someone just hands me a great big jolt of it.

Sunday, April 21, 2013

A dog door-opening solution

I've always meant to document this properly:

We have room-by-room heating, and we have a dog. I've set up pulleys in the rooms we keep warm to close doors behind our dog, and handles he can use to open them. That way, he can go wherever he wants in the house and doesn't leave an open door behind him, letting heat out.

The pulley and handle were dead simple to put together. The handle is just a metal hook like you can find at any hardware store, screwed into the door at nose height with some rope and soft fabric wrapped around it. The pulley consists of two screw eyes, a string, and some socket wrench attachments I had lying around for weights. The string ties to the screw eye on the door, goes through the screw eye in the doorway, and drops down beside the door.

Toby had no trouble learning how to push open the door. It took him maybe a couple days to learn how to pull it open from the other side. He settled on a two-part motion, first swiping the handle with his paw (or with his nose) to open the door a bit and then nosing it open the rest of the way. The only tricky part was getting the amount of resistance just right (by varying the number of weights) without putting him off the concept entirely. Lots of treats.

I used pulleys instead of spring hinges because spring hinges always seem to end up squeaking, and because the pulley seems to give a more consistent amount of resistance.

Thursday, March 21, 2013

To Whom It May Concern:

[This letter I sent to a hospital is about a situation in Seattle, but this is very much a national issue. If it worries you, check it out and get involved.]

I'm a Swedish Hospital NICU parent, and I just received a fundraising letter regarding the Lytle Center for Pregnancy and Newborns. I have great respect for everyone I've dealt with at Swedish and feel that we received excellent care there. However, I will not be supporting this Center, and I would like to tell you why.

The recent merger with Providence Health & Services, a Catholic health care organization, and removal of "elective" abortion services from the hospital leave me skeptical that the Lytle Center will truly provide "convenient access to a full spectrum of prenatal and postpartum care" as described in your letter.

"A full spectrum of prenatal and postpartum care" may necessarily include abortion. It may, yes, include so-called "elective" abortion in a time of extreme duress for parents facing one of the toughest decisions of their lives. This is particularly likely in the case of high-risk pregnancies such as ours was.

It may include end-of-life care, as indeed it did in our case: we lost one of our twin daughters in the Swedish NICU and, at that time, felt well-supported in all of our our decision-making by Swedish staff.

It most certainly, in all cases, includes the availability of contraceptive advice.

I am no longer confident that Swedish can provide these things in a convenient manner, nor that it will continue to provide them at all in the future. I will redirect the contribution that I would very much like to send to the Lytle Center to March of Dimes, instead.

[Upwind Both Ways]

Thursday, January 10, 2013

Pretend Daddy

(My two-year-old started talking to "Pretend Daddy" while I was out yesterday evening, sort of an imaginary friend version of me. I think this is pretty much how that came about)

They found a way in, last night, when I didn't come home until after my two-year-old daughter went to bed. The Clever Ones that usually linger just out of sight around her saw their chance and took it. They fashioned a doppelgänger from her bright, carefree thoughts of me and started to whisper to her. She began to speak of Pretend Daddy.

She says that Pretend Daddy -- "Ysh-Hothur" in the Unspoken Tongue -- sings better than I do. I can only imagine what perversions he croaks to our daughter in that broken language while she sleeps. He's taller than me, too, she says: she can sense the raw force that's there, hidden for now, just barely invisible to adult eyes.

As he binds more and more of her small being to his will, he will be able to gather more of the Clever Ones to him. We've seen this beginning already: her stuffed Burt the Bee now has... friends... with him, in his plush, yellow hive; to call those twisted souls "other bees", as our child does, is to make a mockery of all that is sane.

We ignore this Pretend Daddy at our hazard; he must be dealt with. And, so, we have an uneasy truce, perhaps even a diabolical bargain. 

On the one hand, Ysh-Hothur clearly means to use our daughter as an entry point into this world.  He puts our daughter, our family, perhaps the whole of the mortal realm in deadly peril.

On the other hand, he's really useful at mealtimes. "Look, Pretend Daddy's saying you should eat your oatmeal, too!"

Friday, November 2, 2012

Keeper ∅f The Empty Brain

I was a computer science major in college. It was a small department, sort of a university afterthought, and we all pretty much knew each other. So it was extra surprising when this old guy -- practically a mummy, maybe even over 40 -- showed up in an algorithms class. This was firmly an undergrad class, so he couldn't just be a conspicuously creaky grad student. There must have been some oddball situation to explain his presence.

He was annoying. He asked questions all the time, usually about things no one cared about. You might think the professor would be annoyed, too, but he seemed to know this guy in some way. They'd go on and on about some esoteric bit of junk that certainly wasn't going to help me do the homework.

His favorite question was "what about the empty set?" That needs explaining, but it's simple: in set theory, you can have sets of things (set theory is the best-named theory). If there's nothing in a set, it's called the empty set (see? those folks can name!) and abbreviated ∅. A lot of algorithms have to handle the empty set in a special way. 

So what this winner was asking, over and over, was essentially "how does this particular algorithm handle this thing that all algorithms need to deal with?" It's the sort of question that lets you seem smart without knowing much. We dubbed this guy the Keeper f The Empty Set, or K∅TES. It was catchy -- we had t-shirts printed; we wrote a theme song. OK, not really, but we did roll our eyes whenever he opened his mouth. I mean, why did this guy need to be the center of attention?


This Tuesday, 15 years later, I was a creaky 35-year-old sitting in a classroom surrounded by 20-somethings. This was kind of an oddball situation: I'm taking this class because I need to get accepted into a PhD program that I don't really have the background for. It's a small program, the kind where everybody pretty much knows each other.

I need to prove to the department that I can do the classwork. Here's what I worked out: the professor will write a "recommendation" letter to the department describing my performance in class, however I do. If I do badly, the letter will say "send this dork the thin envelope" and I'll be throwing away the $85 application fee and a whole lot of time. I have one goal, here: impress the professor. 

I talked to the prof ahead of time, so he kind of knows me. I don't have all the background that the kids actually taking the class for credit do, but I have other areas of expertise. So I ask questions that are a little off the topic of the lecture, about related esoteric junk that the prof might be interested in but that won't help anybody do the homework. 

And getting a chance to ask questions is no problem. Turns out -- and, man, I wish I'd realized this a decade or so earlier -- 20-somethings have pretty much zero self-confidence in class! So the prof will ask a question, and there will be silence, and then crickets, and the crickets will complete the entire first movement of Cricket Symphony #3, and then I'll pipe up and try to score some points.

I'm sure that gets pretty old for the other students. What I'm really curious about is the nickname they've chosen for me. I hope it's catchy.