Project idea: improving my attention span

By now it's a commonplace that the internet whittles your attention span down to the sort of tiny nub that only lets you focus on one thing for about thirty seconds before popping away to check email or RSS or Twitter or what have you. Word among my older MIT friends is that burnout and curricular exasperation can have similar effects. I'm inclined to believe them, having lost all patience with, say, biomechanics. *growl* *ahem* Where was I?

Oh, yes. I've been thinking that, among the other soul-restorative measures I plan to take this summer, I should work on reconstructing my attention span. According to my parents, when I was young I had a wonderful attention span, and could admire a pebble for ten minutes together. I'm not sure how much I believe them, but I do feel like my attention span has decreased dramatically over the past couple of years as I've started to read more and more things on the internet.

So I gave myself a test. I had to read something all the way through without looking at anything else on my computer. I picked the first interesting-looking article out of Give Me Something To Read, which turned out to be an NYTimes article about arranged remarriages in China following the 2008 Sichuan earthquake. (Incidentally, the article is very good -- thought-provoking and emotional without being overwrought.) Even though it was interesting, it was surprisingly difficult to get through. My mind kept wandering. Indeed, my mind is still wandering. I've pulled up my chat client once already while writing this blog post, and I keep having the urge to do it again. I'm like Randall Munroe at the typewriter here.

But with summer comes the opportunity to read books again! Do you have any idea how long it's been since I just sat down with a book and plowed more or less straight through the whole thing? I feel like I haven't done that since high school... So, as I pick up books again for the summer, I'll consciously practice keeping my attention on one thing for an extended period of time, and try to avoid get up every five minutes to get food or check my mail. We'll see how well I do, and whether this will translate to an improved studying efficiency in the fall.

Silliness: Legos and BioBricks

It's finals week around here, which means you get a brief post while my brain tries to figure out electroosmosis and Van der Waals forces.

The similarities between Legos and BioBricks are legion -- in fact, if I'm explaining synthetic biology to someone and I've got more than ten minutes of their time, I'll break out my favorite Lego Analogies for the desirable properties that we want biological parts to have.

But they're similar in another way. Everyone refers to BioBricks as BioBricks, but you're supposed to call them BioBrick Standard Biological Parts.

Trumpet fanfare optional. [Source]

Likewise... hope I'm not ruining all your childhoods here... The LEGO(tm) corporation will be very, very sad if you refer to their product as "legos" instead of "LEGO bricks" or "LEGO toys". They might even cry.

Apparently if you went to legos.com, you used to see this before being redirected, according to Mental Floss.

This sort of prescriptivism amuses me a little. I don't know enough about the relevant laws to comment on the legal necessity of being anal about plurals. But I was in a class co-taught by Drew Endy once, so I know he can say "BioBrick Standard Biological Parts" until he's blue in the face. Better him than me, I suppose.

Times when biology knowledge comes in useful

I love pineapple. Really, really love pineapple. Unfortunately, it irritates my mouth. I recently found out that this is not only due to the acidity -- pineapple contains a protease, bromelain. Bromelain will eat your face pretty effectively -- in fact, apparently there's a lot of interest in using it for wound debridement. [visceral shudder]

Unfortunately, the last time I ate a ton of pineapple all at once, I forgot about the protease until it was too late. But then I thought, "aha! I can saturate the protease with another type of protein and my mouth will remain unaffected!" Then I drank some milk.

Bio labs use milk as a generic solution of "loads and loads of proteins" in a lot of techniques. The one that springs to mind is Western blots. Basically, you run proteins through a gel that separates them by size and/or charge, to help identify what proteins you've got in the sample. Then you put your gel onto a nitrocellulose membrane that adsorbs proteins, so the spots from the gel transfer onto the membrane. Next, you want to probe the membrane with antibodies that should bind to your protein of interest, if it's on the membrane, and light up. But what's the problem? Antibodies are proteins, and the nitrocellulose membrane grabs onto all the proteins it touches, so unless you do something the antibody will just bind to the entire blot. What to do? Enter the milk! If you soak the membrane in milk before adding antibodies, then the milk proteins will bind all over the place and saturate the membrane, so then you can add antibodies without fear.

I told Zek about this and she mentioned another method for taking the bite out of pineapple: soak it in salt water. Apparently this is traditional in some places. We speculated that the high salt denatures the bromelain. I have yet to test whether this works or not, and whether it affects the taste.

Meal planning: harder than it looks

Today was ET's Brunch in the Park, an event we throw every year for the current actives and alumni. A bunch of us made various breakfasty dishes. Watching the meal planning and preparation process was quite interesting. Most people went with something very simple, such as "pancakes" or "bacon", where the planning reduces to "Step 1: Buy a lot of whatever. Step 2: Cook all of it." I volunteered to make eggs, but I unwisely decided to get all fancy and make oven scrambled eggs with lots of mix-ins on the side.

My crucial mistake was not bothering to figure out the proper ratios -- I just went to the supermarket and bought "one" of everything: one head of broccoli, one 3-pack of bell peppers, etc. It turns out that one head of broccoli has significantly less mass than three bell peppers. It also turns out that it's hard to pan-fry things when all the stove space is continuously occupied by the pancake makers.

The worst part, though, was that the eggs were far too little and far too late. I cracked 25 eggs, but I should have done two or three times as many (or used an equivalent amount of that egg stuff that comes in cartons). We had around 30 people and only about 10 of them could have gotten an adequate amount of eggs. (As consolation, I can offer the fact that eggs + sauteed mushrooms + fresh basil = awesomeness!)

This episode gives me a whole new appreciation for the work our cook Karen does in planning meals and specifying what needs to be bought. She specifies the week's shopping list very neatly -- 4 pounds of broccoli, 3 cans of butter beans, foo units of bar, baz units of quux. Of course, she's had at least 20 years of practice, so I shouldn't be surprised that she's expert. After all, 2h/meal * 7 meals/wk * 20 full academic years works out to ~ 10,000 hours.

I just hope I can devote that kind of time and energy to some kind of lifetime pursuit or career...

Invasion of the possibly useful jargon

Every time I take a class, I semi-consciously pick up its jargon and use it for all kinds of unrelated things. I'm aware that this is very common among nerds/hackers -- after all, I hang out with lots of them. I, too, speak of "pinging" people in real life, and of the "failure modes" of couches and suchlike. But because I'm a biologist hanging out with mostly non-biologists, it stands out a lot more because everyone else isn't using jargon from their biochemistry classes. I don't know many other people who use words like "inhibit" and "saturation" and "depletion" and "steady state" and "modularity" on a daily-to-hourly basis. (OK, maybe the last two are more widespread than I think, and I just need to hang out with more MechE or EE people.)

The most recent one is "timescale", or "on the timescale of". I picked this one up from my biomechanics class, which analyzes bio-materials of all different sizes from single molecules to whole organs. In order to keep ourselves sane, we have to take into account the size of the object in question when choosing an analysis method. Should we speak of the stresses and strains in a rod made of continuous material, or of the entropy-driven behavior of a randomly meandering chain? Can we ignore thermal motion of molecules, or the transient behavior when you begin applying force? It all depends on the length scale.

I find the word "timescale" very useful in my daily life. It's much easier to say exactly what I mean if I say "on the timescale of weeks" rather than "in the medium-term". I would love to say that it helps other people understand, as well, but unfortunately no one else seems to have picked up on it yet, so I will have to wait and see.

Strangely enough, the jargon-adapting habit seems to be largely involuntary. However, the success or failure of a given word is definitely related to its usefulness, to the usefulness of the metaphor. There's not that much difference between a feedback system in a cafeteria and a piece of complex software, so it makes sense to speak of both of them as having "failure modes". I guess this is what the "seeing-as" theory of intelligence is all about. (Something I read in one of Hofstadter's books... I don't remember which it was, and I don't know what this is all about.)

Addendum: jargon-adapting is also not particularly widespread among people who aren't part of hacker or twinkie social circles. Or, at least, I don't encounter it very much, and I often get laughed at (in a kind way) when I'm hanging out with my friends from Bioengineering and I speak of rainwater "saturating" a drain, thus forming a puddle.

Exhaustion

This semester, I've been mentoring a team of two freshmen working on designing a cooperative system of biofuel-producing algae and nutrient-recycling bacteria. It's a really neat project -- in fact all three of this year's 20.20 projects are really interesting. They have more of a focus on system dynamics / population engineering, where my year we focused on devices. I think this may be due to having Ron Weiss instead of Drew Endy. (Another indication of Weissitude is that we're all modeling our systems in MATLAB... sigh. I am not fond of MATLAB.)

I don't actually know much about biofuels, synthetic cooperation, or complex metabolism. I also don't know much about mentoring a team in the sort of hands-on, hands-off style that's appropriate when the point is for everyone to learn and stretch themselves. So it's a challenge, but an extremely satisfying one. I have watched my team drink the synthetic biology Kool-aid in the most remarkable way. There was a palpable transition from naivete to relative understanding;

Mentorship is important, but providing it at this level is also exhausting. Every day after class I feel physically tired (actually, that may have more to do with my sleep schedule than my mentoring schedule).

Gaze Direction, or How Your RSI Prevention Software Can Distract Other People Too

The other day I noticed something funny happening. To set the scene, recall that humans are wired to detect other humans' gaze direction as a method of figuring out where the important stuff is happening at the moment. Robots are working on this too.

For the last several months I've been having problems with eye strain after using my computer for too long at a time, so I've been using RSI prevention software to remind me to look away from the screen every so often. (I use TimeOut (review here) because it doesn't reset its timer if you leave the mouse alone for 10 seconds while you're reading something.)

When anyone else is in the room and I look up from my laptop to stare fixedly at the opposite wall, about half the time they will look up too, wondering just what is so interesting about that light fixture or Periodic Table poster. It usually takes them several seconds to figure out that I'm not actually looking at anything in particular... we're just so used to thinking of gaze direction changes as highly meaningful.

Of course, this indicates to me that almost everyone I know needs to look away from their screens more often. Do it right now (seriously, I don't mind waiting) ...................................................................
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you'll be surprised how your eyes feel when they refocus.