Thursday, August 24, 2006

Fatherhood, week 1

[Baby stuff, probably non-interesting unless you're family =)]
Miscellaneous notes, after being a father for a whole week:

- Baby swing = Crazy Delicious Baby-Sleep-Inducing Machine.
- When changing diapers, it's generally a good idea to cover "the equipment" with a wipe, otherwise you may be treated to an in-house version of the Bellagio Fountains. With yellow water, and without the lights and music, though. That said, it's worth -not- taking that precaution just once, to see the look of surprise when he pees himself in the face [No, I didn't do so intentionally, it happened when I accidentally forgot to cap the waterworks.]
- Zander will soon be ready to challenge the strongest boy in the world to a wrestling match and utterly dominate him. Why ? Because, in my unassailable dad logic, I note that he can already lift his head up and turn it while lying on his stomach, something that apparently generally doesn't happen until the second month, and conclude that he must be extraordinarily strong.
- The lack of sleep, and overall stress level, hasn't been as bad as I feared ie we haven't been reduced to bone-tired bundles of nerves [yet]. That's attributable entirely to the fact that Zander is a great "starter baby" for rookie parents -- he sleeps quite a bit, doesn't fuss very much when he's awake, nurses well, and is pretty forgiving of clumsy parents who take a bit too long to change his diapers or clothes.
- One of our strollers has been named Optimus Prime, in view of the fact that it can be transformed from a full-fledged, large stroller into a fairly compact cuboid with the simple press of a button and a small amount of leverage applied in the right direction. It might be possible to turn it into a tandem bicycle with the right series of pushes and pulls. I suspect it was designed by origami masters capable of accessing hidden spatial dimensions.
- My man's got flair even when he's asleep:




















In summary, it's pretty cool being a dad. How could you not love a face like that ?

Saturday, August 19, 2006

A description unlikely to lead to future interview requests being granted

From a NYT Magazine article describing the rivalry in competitive surfing between Kelly Slater and Andy Irons:

"Irons is considerably bigger, with a hint of baby fat and the blank, open-mouthed stare of a healthy young animal."

Ouch.

Friday, August 18, 2006

Alexander (Zander) Foli Todd Mallet

The eagle has landed. I repeat, the eagle has landed.

DOB: 9:41 AM EST, 8/16/2006
Weight: 9 lbs 2 oz [4138 g]
Length: 21 inches [52.5 cm]
Feet: Huge
Cute Factor: Off the scale. Cutest baby in known universe, confirmed by several leading independent baby cuteness research institutes.

Pictorial evidence for above claims:




















































Other items of note:

- Driving down an extremely windy, narrow road with no median between the two directions of traffic [the Jamaicaway in Boston], at 11:30 at night, with your wife writhing in labor-induced agony beside you is a little ... nerve-wracking.
- Christina is an absolute champion for pushing out a baby weighing quite a bit
more than the average [Yes, I know it's the distribution for Norwegian babies, but if it's good enough for the NIH, it's good enough for me ;-)]. Pushing, for all men who, like me, had no clue what it really involved goes like so: contract all the muscles in your body as strongly as you can, while holding your breath for 10+ seconds; take one breath; repeat muscle contraction + holding breath 4-5 times. Relax for a minute. Do it all over again. For several hours. Oh, and by the way, while doing this you're in a ridiculous amount of pain, drugs or no drugs.
-
We have verified full function of Zander's food input and waste output ports.
- Yes, I'
ve changed diapers. Most of them so far, actually. And I've already been christened -- he peed on me the very first time I changed his diaper. Nice to meet you too, dude.
- Do not, I repeat, do not put toothpaste on your baby's butt instead of vaseline. I almost made that mistake because, in the fog of diaper war, the two tubes looked pretty similar. Thankfully, I realized the error of my ways before actually slathering minty-fresh toothpaste all over his little posterior.
- Zander currently has only two states: eating or sleeping, with very quick and easy transitions between these states [Thankfully ! Let's see how long that lasts ...]. He is also not a man to let a full breast go to waste -- he nurses like a champ.
- Your ob/gyn may be gay if, in talking to you about your labor, he quotes lines from Barbara Streisand songs, namely: "What's too painful to remember, we simply choose to forget." Simply outstanding.
- I was under the impression that the good folks at the hospital will assist you in installing a baby car seat base into your car. Not so. All they do is tell you how to do the easy part: strapping your baby into the car seat, which is about as necessary as the little recorded message at the beginning of a flight telling you how to fasten your seatbelt. To get a "certified" car seat installation, you have to go by a police station. After driving to the two nearest police stations with a jury-rigged installation and finding out that we needed to make actual appointments, we decided to call it a day and just head for home. Parents for only two days and we're already being cavalier about our baby's safety...

In any case, we're back home and settling in. More dispatches as deemed relevant.

Tuesday, August 15, 2006

A perspective on science-induced pain

I've been reading some of the early papers about T7, starting with papers published almost 40 years ago. Apart from the "Oh, so that's how & when they figured that out" factor, an equally interesting facet is that reading these papers with the benefit of the current state of knowledge means seeing science in action, so to speak -- watching the transition from early ideas [with varying degrees of "correctness"] to our current understanding, with various course corrections along the way.

Certain paragraphs also serve as a sharp reminder of the fact that, not too long ago, scientists had to walk barefoot, blindfolded, through snow, uphill both ways, to figure things out. Consider the following excerpt [from here]:

"Weiss and Richardson (1967) have shown that the 5' end of the poly-G-binding strand terminates in pApG----, and the 5' end of the complementary strand terminates in pTpC----. It is also known (as discussed extensively by several workers in the Cold Spring Harbor Symposium on The Genetic Code, Volume 31, 1966) that RNA chains grow in the 5' to 3' direction, protein chains grow from the amino terminal to the carboxyl terminal end, and translation of messenger RNA proceeds from 5' to 3'."

In other words, around the time this paper was published:
- Determining the last/first 2 nucleotides of a DNA sequence was considered a genuine scientific achievement. Systematic sequencing was still almost 10 years in the future, and the sequence of the first bacterial genome was 20 years away. In contrast, nowadays if you're not determining [and analyzing] millions or billions of nucleotides, you're not doing anything noteworthy.
- The details of how proteins are encoded in DNA, and the direction in which DNA and RNA are "read", had only been established 3 years ago, and was worth discussing at scientific conferences. This is stuff that kids learn in high school today.

Summary: biology was Really, Really Hard back then, and we didn't know very much, which must have meant a lot of fumbling around trying stuff. And yet people kept at it. I suppose the lesson is that I should stop whining about lab work and just get on with it, so that 40 years from now, my grandkids can say "Wow, you guys didn't know that back then ? How did you manage to do anything ? Hardcore !" before flapping their bio-engineered wings and flying away.

But it also brings up questions: is science-induced pain conserved ? In other words, are we now trying to do things/answer questions that are so much more complicated than what folks X years ago were doing that, despite our increased knowledge and technical capabilities, the work is still just as difficult ? Is there a minimum level of knowledge and technical capability below which doing stuff is order-of-magnitude more difficult, and above which the pain stays pretty constant or even decreases ?

Monday, August 14, 2006

D-day has arrived

Today is Christina's "official" due date. Unfortunately, due dates are just another instance of seemingly-precise data that actually have fairly low information content, because a due date is very loosely correlated with when the baby will actually be born -- 90% of first-time mothers deliver after their due date. It's looking reasonably likely that Christina will be among those 90%, although maybe our midwife will say something different when we go see her later today.

This brings me to a more general point about pregnancy that I didn't fully appreciate earlier: nothing is certain. Pretty much the only thing that's guaranteed is that the mother-to-be won't sprout an extra limb [externally, at least], but everything else is up for grabs -- whether she has morning sickness or develops weird food cravings, how much weight she gains, what size the baby is going to be etc. In retrospect, we might have been able to spare ourselves a few prenatal visits
because the vast majority of the answers to our "Is this normal ?"-type questions boiled down to "Everybody is different", which in plaintext means "We're not really sure. Call us if she wakes up one morning and is suddenly 7 feet tall and has a beard." In more fancy words, the probability distribution of just about every phenomenon associated with pregnancy has heavy tails.

Another lesson learned over the last few months: there's nothing like a prenatal visit for making a man feel invisible/irrelevant. It starts out in the reception area: every available magazine has a title made up of some combination of the words "Baby", "Parent[ing]", "Healthy", "Happy", "Infant" or "Mother". Men, when they are mentioned, usually occur in phrases like "How to make sure your husband doesn't drop the baby". I'm not saying I'd like them to have a bunch of issues of "Trucks, Guns and Hot Chicks" lying around, but it sure would be nice to have magazines other than ones that are so obviously not meant for men. And it gets worse when you see the actual midwife/nurse/doctor -- generally, I wasn't even acknowledged via a "hello" when this person came into the room, they just looked straight through me and started talking to Christina. Again, it's not that I want a cookie and a pat on the head for accompanying my wife to a prenatal visit, but it sure would be nice to be treated with an attitude conveying something other than "Oh, so you're the one who did this to her. Are you happy now ?"

And the final take-away from the last few months: it's a good thing I wasn't the one who had to be pregnant, because I don't think I'd have had the patience to deal with all the attendant aches and pains. Christina, in contrast, has been an absolute saint -- never once did she become the bitchy, moody person that pregnant women are so often portrayed as. But even sainthood wears thin -- she's very ready for the baby to arrive, and so am I.

So: time to leave the cocoon, little man ! The wide world, warts and all, awaits.

OMG, that crazy president totally has a blog !

Iranian president Ahmadinejad apparently now has a blog [via BoingBoing]. Between this and his letter to Bush [awesome typo in the translation: the Bush slogan is supposedly "War and Terror"], he's certainly using heretofore non-presidential forms of communication. It almost seems like he's watched one too many movies of the sort where a common-sense "man of the people" who tells it like it is winds up as a politician and then proceeds to turn the established order upside down by departing from precedent and doing things his way [examples: 1, 2]. Maybe he'll set up a MySpace page next so people can "friend" him.

One thing I know for sure after watching an interview with him on 60 Minutes: not a man who should have a nuclear weapon. [Not that I really want anybody to have nuclear weapons ...]

Wednesday, August 09, 2006

Year II: lessons learned

The last couple of weeks have been full of milestones: the second anniversary of our move to Boston, my qualifying exam, Christina's birthday a couple of days ago, and 2 years since my first blog post. And, of course, our very own little person will hopefully arrive in the next few days. With that, I figured it might be worth to put together another summary post of the past year, though this one will be much shorter than the multi-installment summary [1, 2, 3, 4] that I did last year. So, here 'tis.

"Shhh, be vewwy, vewwy quiet, I'm hunting theses"
...
and I had almost as much trouble finding a thesis topic as Elmer has with that wascally wabbit.
I looked into working on microRNAs, tried to come up with a good reason to rebuild a yeast chromosome, started working on investigating transcriptional feedback in the yeast pheromone response, and finally settled on working on T7.

One obvious question is why I had such a hard time finding a topic. The answer is also fairly obvious: my first choice [working on malaria] wasn't an option, and it took me a while to find an acceptable alternative that coupled my other two main interests, synthetic biology and high-throughput [HT] data generation and analysis. Those two areas are not natural bedfellows because most work in synthetic biology is currently focused on building single instances of relatively simple systems [which don't generate much very much data]. This meant that there were relatively few examples of research
that I could use as inspiration, and so it took me a while to formulate a topic that fit my desires, addressed interesting questions, and fit into the overall research direction of Drew's lab.

In retrospect, I thought finding a thesis topic would be one of the easier parts of grad school. Guess I was wrong.

"It's what you don't know that's important"
A large part of getting a grip on a given field is having an idea of what the current limits of the field are ie what isn't known, what the interesting questions are, what's difficult etc. These aspects are, of course, the very bits that aren't covered in class: you're told in excruciating detail what is known, but nobody dwells on the "Hic sunt dracones" areas, even in graduate classes. I think a large part of the point of grad school is precisely that you figure out where the boundaries of knowledge are in your attempts to push them a bit further.

In any case, when I started school, I lacked the basic "this is what we know"-type knowledge and had no big-picture perspective of the current challenges in biology either, beyond a fuzzy "Biology is hard, because, well ... people tell me that it is. If it were easy, we would have created a dragon by now." Lacking this mental scaffold made it difficult to get more than a superficial understanding of the papers I read and talks that I attended -- not only did I struggle to fully understand the claims/results contained in the paper/talk, I also didn't have a framework in which to evaluate the overall impact of what I was being told. The end result was that my takeaway was generally "Uhm, ok, if you say so", and a few isolated facts that didn't really connect to the bigger picture.

The biggest intellectual transition for me over the last year was moving beyond the "just the facts, ma'am" stage, and towards a better meta-level understanding of at least a couple of the sub-areas of my new field. The largest contributor to that increased understanding was actually my thesis odyssey. In the process of trying to formulate a thesis topic, I had to think really hard about various areas of systems/computational biology -- what questions were being asked [and why], what tools were available to answer them etc. Doing so helped me tie together a lot of the loose strands waving around in my head into a semi-coherent overall picture.

The negative aspect of all this cogitatin' and meditatin', of course, is that I'm not as far along as I would have liked to be after two years of school -- I haven't done anything yet. That said, probably the main reason that I'm [theoretically, at least] "behind schedule" is that my envisioned timeline radically underestimated the switching costs of moving from computer science into biology -- remnants of the instinctive "Oh, how hard can it be ?" programmer's reflex, possibly.

Integrating over everything
At the end of the day [or year], though, the high-order bit is that I [still] like what I'm doing and think I made the right choice in leaving MS. That's not to say I didn't have a few "It'd be so nice and easy to go back to software" moments during and after our trip to Seattle -- things like hanging out with friends and family, going by the motorcycle shop where I spent many a dollar buying unnecessary stuff for my bike, and checking up on our house in Seattle served as sharp reminders of everything we gave up when we moved here. I'm sure I'll have similar sentiments each time we go back, but hopefully/presumably their intensity will decrease as I get closer to the end of grad school and can see the light at the end of the tunnel.

Next up, year III: try to get some real work done while being dominated by a tiny lifeform halfway based on me.

Monday, August 07, 2006

The ultimate rejoinder

Tuesday, August 01, 2006

Just for the record ...

... and in case I haven't clearly expressed my opinion on this matter before: Boston sucks.

Why ? Because we've had to spend all day cooped up inside due to a heatwave. And it's not about to get any better:

Tonight: Widespread haze after 3am. Clear, with a low near 80. West wind between 14 and 16 mph.

Wednesday: Widespread haze. Sunny and hot, with a high near 101. Heat index values as high as 111. West wind between 14 and 20 mph.

Compare that to the weather in the Promised Land, with daytime highs in the 70's.

Yup, signs point to "Definitely sucks".

Time to really get cracking on the research front, so we can leave this godforsaken place asap.