[M]etabrain [E]ntry [L]og - Braindump of the Mel. Seek coherency and relevance at your own risk.

Polyglot content on the OLPC

Spent a good chunk of yesterday at OLPC re-teaching myself how to program in Python while making a library translator. I’m beginning to learn about internationalization, and spent far too long reading about gettext and now know why there are so many underscores inside printfs (print statements in the C language).

The short answer is that they allow substitution of strings within programs - for instance, _(”Hello!”) transforms into “Hello!” when you tell your software to build with English, and “Ba’ax ka wa’alik!” when you tell it to build in Mayan. When it’s called, gettext performs a lookup-subsitution in the .po files you give it, which are basically lists of phrases you’ve got inside your program, written in a bunch of different languages.

.po files are apparently very widely used because they’re so simple (they’re literally just lists of translations of phrases in your program), but they break down when you try to translate larger bodies of information because there’s no way to build structure into them. Every message has to have an unique ID. If you’re building something on the scale of - say, the OLPC library, that’s thousands and thousands of reference numbers floating around with no way to categorize them. Ouch. Okay, you could specify the format of the msgid and parse it to create a structural hierarchy, but… really, there must be a better way. Any ideas?

As part of translating the Biology page (read: while putzing around before writing the actual code that would translate the Biology page) I tried experimenting with XML to replace .po’s and it seems to work. Kent Quirk pointed out that Python dictionaries would do the same thing (and they’re what I’m using now), but the benefit of XML is that you can enforce template compliance with a DTD to make translations less random and spotty (like, you can’t put in three different translations for the title in Spanish, you have to pick one) and it also fails more gracefully in case someone messes up while hand-editing… and translators are going to be hand-editing these files.

There’s also Wikipedia’s approach to multilingual coordination, which (as best I can tell) is “put lots of links to variants in different languages and let people figure it out and hand-link it themselves.” Weirdly enough, each language’s wiki is completely separate from the rest, meaning I’d have to create a separate account to edit the Chinese and English wikipedias. I see the rationale behind the split for content organizing reasons, but the inability to merge different accounts must be annoying for frequent translators there.

But yes. I learned a ton, I had a lot of fun, I started flaking the rust off my high-level programming fingers again (resulting in painfully slow coding yesterday, but it’s getting better) and I’m going back. Hopefully over time my helpfulness-output will start outweighing my asks-stupid-questions-that-take-time-to-answer input. Hurrah, laptops!

Friday, March 30th, 2007 | Uncategorized | 2 Comments »

[root@mel ~]#

This was one of those “I’m going to start typing and see where it goes” things. Chandra was right - I do describe myself as a computer a lot.

I am a homunculus, small and lithe and light, a flurry of happy activity with fingers and toes dancing over control knobs, spine twisting and stretching to reach levers, tiny sneakered feet dashing between displays in my head. A complex system of sensors and cameras and knobs twiddled by me, all running through the programs that I’m continuously rewriting - a system created by me in order to control something far more complex than my capacity to directly handle. It takes all this input, processes it, and and transmits the results out to her.

She’s me, but she’s not quite me. I’m the meta-Mel, the one that sits in the back, watches from above. She eats lasagna, runs in circles, and trips over cables in darkened auditoriums; she dances around classrooms to burn off excitement, screams Keats and Wordsworth and Frost into snowstorms because it feels good to scour your lungs out with poetry, and cries quietly in her room when she’s depressed. She does things spontaneously; she sings, she laughs. I laugh also, and I am happy and sad, but I scurry around her cranium deciding whether to display it or not - I watch, I wait, and I decide who to be. I’m the only one of the two us who can.

It’s taken a while for me to obtain this control. Remnants of a past era, when I was young and still patching together the bulk of this system, still pop up from time to time - PLEASE INSTALL PARENTAL PATCH #255. FOR SECURITY PURPOSES. I ignore most of them. I’ll take the ones I deem useful - sure, a cell phone is a useful accessory to have, thanks Mom - and politely file the rest away, or delete them. They used to be able to override the system. It’s less so now; I’m gently stepping down administrative priveleges, gradually chmodding the files of my finances, my education, my life - from 777 to 744 or 700. Mine. She can still access all this, of course. She has sudo privs, but I am the sysadmin.

My processes run quietly in the background. She’s always the first impression people see. They live with her, work with her, get to know her - and they actually can get to know her. She’s a person, not a mask; she doesn’t try to control what she presents herself as. She can’t. She’s an open book by nature. We operate asynchronously, she and I; she can be her own person without me, just as I can wander off without her, but not for long - we are separate, but symbionts. Without the other to feed off of, neither of us would last too long.

Some folks will catch a glimpse of the control room, or ask to see it, or maybe she’ll mention it to them in a tone of amusement, as you’d show your new dev kit to a friend. I’m more than happy to take them on a tour. Look, this display; see, these levers do that, and if I press this button you’ll see a flashing light in the left corner. A museum tour. Sometimes I’ll even make it interactive. Can you read off the screen for me? Okay, thanks - now toggle the green switch, and spin the red knob all the way to the right. Excellent. See what that does? Thank you. Next exhibit.

Sometimes I’ll even ask people for advice on how to fix things, how to re-hack things, if I can patch their code snippets into mine. Here’s my wiring; can you see where I messed up? Did you figure out how to make yours wake up earlier in the mornings? Here, take this plugin; I made it to teach her how to play piano. But she is mine, always mine, mine to make and control, mine to play with, mine to hack.

And I do. I overclock her all the time. Push the limits of the hardware, the software, my own ability to multitask and control. Sometimes I push too hard; she goes erratic, stops eating, doesn’t sleep, her attention slams hard out of equilibrium and oscillates wildly until it trips a breaker or I pull it down. She’s always running hot. The whine of huge fans is constant here, trying to drown out the noise and the babble that’s always pinging around the cranium; warm jets hissing from vents and grills, and I’ll rub my wrists in the mild heat when they get sore from long hours of pulling knobs and watch her go. Or I close my eyes and let her run entirely unwatched for a while. It’s always amusing to see where she ends up taking us.

Wednesday, March 28th, 2007 | Uncategorized | 1 Comment »

Mel learns to meditate (or tries)

I’m sitting cross-legged with a cushion under the posterior part of my posterior, hands on my knees, back hypothetically straight. It’s just half an hour of meditation. I can clear my mind for that long, right? Or I could count to 1800. 1800 is a small number.

Mind clear. Breathing steady. Bliss! Boredom. Are we done yet? I open my eyes and realize three minutes have passed. Crap. My neck starts tilting from side to side of its own accord. I stop it. Then I realize my hands are tracing small circles over my knees. I stop that. A minute later I start rocking back and forth, hungry for some kinetic sensation. Stop.

Stop; breathe. Breathe, count, breathe. I count 1, 2, 3, 4, and visualize the numbers in my head. Wait, what typeface was that? Bitstream vera sans mono doesn’t have serifs! Delete that serif… that looks much better- damn, what am I thinking about? 1, 2, 3, 4, 5, 6 - that 6 is from Arial, and why does the ascender- argh. New tactic.

Eyes open. Look around the room slowly. Everyone else is sitting still, breathing blissfully. I sit still. A screaming starts in the back of my mind. When I feel antsy and force myself to sit still, there’s always screaming in the back of my mind; at least one part of me is still shouting as loud as possible. (Apparently, this is not normal. I did not know until last week this was not normal.) I want to move. It felt good this morning when I danced and leapt across the floor, and good last night when I drummed until my palms were red and sore. I want to do that again. But I’m sitting still now, breathing.

…and picking out the individual voice-lines for an a capella arrangement of “Smooth Criminal.” WHAT THE HELL. I try to drown the Michael Jackson out by concentrating on my breathing, and I count again. 1 - ah, I’m distracted. 1, 2, 3. 5, 8, 13. I’m digging my fingers into my knee to keep track, but I’m out of fingers now - but I can do it in binary, so I do that, drumming the Fibonacci sequence in binary onto my knee with my fingers. Not entirely sure how this happened.

To make matters worse, I’ve slid forward off my cushion onto the floor and I’m rocking back and forth again. Gotta focus! Gotta stop. I breathe. I still my fingers. I open my eyes. I watch the clock hand go around. And again. I want to see the mechanism inside. (We’re lasercutting clocks in the Wellesley class I’m TAing.) I need to get trained on the laser cutter. (Could you lasercut OLPC peripherals in a Fab Lab?) How do you organize an open source community? (My head drops downwards in thought.) Hey, my socks don’t match! (I… am really bad at this concentration thing.)

This goes on for about another 15 minutes until the instructor chants the final “Om,” which is like a merciful beacon to me because now I can move and look around without feeling guilty. The thing is, this happens whenever I try to concentrate on something for an extended period of time (note the word “try” - sometimes I slip into something and get lost in it and don’t have to try, but good luck breaking me out of that work-reverie. Apparently this is also not normal. I also did not know until last week this was not normal.) I feel like my brain is generally trying to implement spread-spectrum frequency hopping and failing gloriously - that all this thought is radiating off, getting lost, because it has to spew somewhere.

Someone once described me as an “outdoor cat.” I’ll wander in and out when I’m hungry, but you generally can’t find me. My brain’s like that too. An outdoor cat. It’ll cuddle in your cranium once in a while, but when it gets in a feral mood, then - I have to run around the building, or pace the hallway, or play piano, or something, in order to even be able to work. I wonder if learning to meditate would help me, if I can find a way to do it that won’t frustrate me.

Or maybe I can just give up on meditation and learn how to dance and drum instead.

Tuesday, March 20th, 2007 | Uncategorized | 7 Comments »

Where by "artifact" I mean "engineering toys."

I’m doing a research project on engineering education that’s looking at how middle and high school students use physical artifacts to learn about technology. What kind of tools do teenagers use to learn engineering and how does the design of these artifacts affect the kind of learning that occurs with them (what features do they have? do they cater to visual learners? experienced programmers? traditionally underrepresented minorities in technology? students who might have difficulties in “normal” classrooms?)

The following is one part (approximately 33.3%) of a scholarly paper I’m working on; this is an overview and call for help with the “library” section - the other two sections focus on the effect of artifact design on student-artifact interactions and the usage/effect of artifacts in classroom settings, respectively, but I’m focusing on this one for now.

The short:
If you were designing a section of a library dedicated to helping teenagers learn engineering, how would you create the space, choose the materials, and run the whole place, and why?

The long:
In particular, if you were including toys (electronics kits, building sets, K’nex, bot competition kits (Vex?) books, soapbox racers, mindstorms…) how would you set them up in a system that would give you as much kid-learning as possible for as little librarian-trouble as possible (parts getting lost/broken, students not knowing what to do with them, etc.)

The little I’ve seen with engineering toys in libraries so far amounts to sticking gadgets in bins on the shelves and treating them like “normal books” for checkout, but there must be other ways to do this - I’m looking for everything from informal brainstorms to personal anecdotes to suggestions for books and papers to read. (I’m also looking for folks to interview by phone, email, or anyplace reachable by car from Boston - especially librarians and high school students.)

The explanation:
It’s not just the design of the toys and tools themselves but the space they’re within and the people within that space who shape how kids interact and learn with them. A library is a fantastic space to learn within - no schedules, no set subject boundaries, space to explore, and librarian-mentors around to help you find information so you learn how to teach yourself things. What would a teen library for engineering education look like? As a librarian, how would/do you use “engineering toys” as ways to promote and teach information fluency?

The obligatory disclaimer:
I’ll be using this information for my studies in engineering education, and will give you full credit for contributions and cite you however you wish (requests for pseudonyms or anonymity will also be honored). The paper will be licensed under a creative commons attribution-noncommercial-share alike license when it’s finished in May, and I’m working on ways to share it in draft form before then. If you’d like to contact me outside the comments, drop me a line at mel [at] students period olin period edu.

Sunday, March 18th, 2007 | Uncategorized | 4 Comments »

In lieu of whining

I feel like whining (I’m hitting serious physical, mental, and emotional walls right now) but after this sentence I will stop feeling sorry for myself.

There, that’s better. I’m going to try to clear my brain now, and just watch, and write what I see.

I’m watching the shadow of a spiderweb rattle against the wall - it’s trailing in the few inches between a light and the paneling, and draws a quivering black line above a framed inkjetted picture of Franklin W. Olin (you can see the scan lines and the paper buckling from when the ink was liquid).

Now I’m looking down, into the fireplace with faux logs and a tilted metal grille above that deflects the radiant heat out onto my knees and the back of my laptop. There’s a little lick of yellow jetting out of a sheet of blue. The faux logs are hot enough to grow red. It doesn’t look like tongues of flame - they’re too soft and flickering too rapidly to be tongues. I see sheets of atoms wrapped up in their own reactions, throwing blanket of photons around themselves outwards, then swirling and slinging them out, sending an image of warmth onto my retinas.

My eyes bask in a faint heat of tiredness when I close them. I’m typing with my eyes closed now, leaning into a gigantic beanbag chair. I can feel my hands on the keyboards with the little “home key” nubs under my index fingers when I rest, my wrists stuck to the front of the laptop plate with sweat. My right shoulder is crunched up against my ear. I shake the elbow out and relax it. My back tingles with a slight ache. My feet are warm. I feel simultaneously light and heavy and pained, and a little bit floating. My toes are braced against the ledge of the fireplace.

When did my knees start aching? Why do my hips feel cramped like they haven’t been stretched in ages, and why does my neck feel like it has been stretched, just in the wrong direction? Why does my body feel so old on the inside?

Wow. I really am bad at taking care of myself.

Thursday, March 15th, 2007 | Uncategorized | 1 Comment »

Help me figure out an algorithm?

CNN Money has a neat page that lets you “rank your goals” (up to 15 of them) by pairing them up and asking you to choose between them.*

I was surprised that the option of having a family someday (not like I’m, y’know, dying to marry and settle down, but that I want to have that option if the right person comes around) ranked so highly, and that graduate school ranked so low. I suppose if I’d put “become a professor” instead it would have pulled it up some, but there are many things I value more than formal academic credentials. (Sherra Kerns tells me that I’ve got to at some point “pay my dues” if I want to be an engineering prof at a top-notch school. I told her yes, but that I wasn’t ready to pay them right now.)

Anyhow, my randomly generated list, which is a rather poor approximation of what I’d actually like to do with my life… but makes for an interesting set of information anyhow.

*yes, I did go back and try to figure out what sorting algorithm they’re using in the 5 minutes before my next meeting. My first thought was quicksort, but the big-Oh is less than n^2 log n and more than n log n. I’ve got to run now but I’d like to puzzle this through - I don’t think it should be this hard but my brain’s fried from not sleeping for two weeks… any suggestions?

Big-O table, for reference
# of items : # of questions
2 items = 1 question
3 items = 3 questions
4 items = 6 questions
5 items = 10 questions
6 items = 15 questions
7 items = 21 questions
8 items = 28 questions
12 items = 66 questions

Wednesday, March 14th, 2007 | Uncategorized | 2 Comments »

What’s your frequency?

Warning: another one of those posts that has no topic, no point, and is mostly a train of thought. Yay!

While searching for an email address I ran across an old one I sent to the ICB class I was TAing for more than 2 years ago (the current juniors when they were first-semester freshmen). Somewhere in the midst of talking about line integrals and FresnelC is this snip:

Engineering is the art of being lazy. So before you brute-force someothing, remember that your brain is the best tool for being lazy, and do your best to use it before you tell the computer to go chug.

Looking at all the emails I’d sent to the class, I was stunned by the amount of time and energy I’d put into teaching in the last three years. It’s something I’ve been struggling with for a while (in the past two weeks I’ve had at least 5 conversations with different people explicitly directed at this topic). Have I been putting so much of myself into the education of other people that I’ve neglected my own? “I think that you can do anything if you stop trying to do everything,” one of my friends said. “You need to change that conception [that you waste people's time] of yourself and start thinking you’re worth it, dammit.” For some reason, I think my time is worth being wasted for other people, but their time isn’t worth wasting to teach me.

Last night when our SCOPE team returned from a marathon 5-hour design review (which was preceded by a marathon 72-hour shift in our lab - you’ll see us staggering around today after having gotten more than 3 hours of continuous sleep for the first time in a week or so - but IT WORKED! IT WORKED!) I stopped by the library to return some stuff and inadvertently ended up reading a book while I was there. It was one of those “parable” stories of how some person changed their life as a way to indirectly (supposedly) get you to change your own.

In the book, one of the characters (Agnes) does a demonstration at the dinner table by way of explanation. She turns on a badly tuned radio and raises the volume until everyone is covering their ears and wincing at the terrible static. Then she turns the volume off, tunes the radio to a jazz station and slowly raises the volume again. This time everyone’s tapping their feet. People are like radios, Agnes says. If you want to amplify your actions and your effect on the world, you’ve got to make sure you’re amplifying the right thing - tuning in to the right frequency that is what you’re all about. Do what you love in the service of people who love what you do.

They all go around the table talking about their “fundamental frequencies” - one is about “service,” one is about “nurturing,” another about “freedom.” Those “frequencies” manifest themselves in the intents of all their actions. For instance, the “nurturing” person became a hard-driving business mogul, but did it in order to train her subordinates to grow as people and eventually branch off and start companies of their own - the “freedom” person was a consultant (creating more freedom for himself) who, through his work, made others more aware of the choices they could make for themselves (freedom for them). According to the book, one’s “fundamental frequency” comes through in everything you do, no matter what career you’re in, whether you’re talking about your personal or work life, everything.

So what’s mine? Teaching? That was my first thought, backed up by the inane amounts of email I found to former students. But that can’t be the fundamental. I was happy way long before I started teaching, and spending all my life in a classroom doesn’t excite me - I want to spend some of it in a classroom, but I want more.

Learning? I learn best by teaching. I love searching for new facts, asking stupid random questions, reading like a little fiend in the middle of the night. But no, that’s not quite it. It’s too much of a one-way draw. I do (and love) a lot of things that I don’t accrue any learning from, like building webpages for random groups, accompanying singers on the piano, stuffing envelopes to help a staff member out.

Service? No, more specific; I only like serving people in several specific ways - but what ways? Love? Well… all right, but of what? Again, too general. Information? Closer, but no. I don’t like accumulating facts. Information overload is something I fight with all my might - I strongly believe there’s no sense in having tons of data that doesn’t mean anything and obscures the things that do mean something - I see information as “dead” and “alive” when I look at it, like how some people see “dead” and “alive” shapes in Conway’s Game of Life, or in Go. Information that’s dead is useless. Information that’s living, that means something, can grow, is good.

Then something Dee Magnoni said earlier flashed through my mind. She’d been describing the role of a librarian. “…to move things down the spectrum from information to knowledge.“

Knowledge. Information that has meaning. That sounds about right. Getting knowledge. Transforming information into knowledge. Creating knowledge. Helping other people obtain it. The power of knowledge - the service of providing knowledge, the freedom of having knowledge. That really does sound about right. At least it’s the best approximation I can provide right now, and it works for me at the moment.

What’s your frequency?

Tuesday, March 13th, 2007 | Uncategorized | 1 Comment »

Academic freedom and political correctness

Happy brain note: Digging around on Schroedinger’s Equation with Ryan this morning after yesterday’s dinner conversation with Chris Morse (apparently, this equation has something to do with stable arrangements of electrons in valence shells), we found the usage of Bra-Ket notation, which Raymond was talking about the previous day in the MetaOlin communications module. I’m now trying to figure out what the heck Bra-Ket notation is and how it’s applied to both realms.

And an interesting tidbit on academic freedom from the Chronicle of Higher Education. The article was discussing the Larry Summers and Ward Churchill cases. Churchill was a professor at U Colorado Boulder when he wrote an essay describing the WTC workers on 9/11 as “Little Eichmanns,” claiming they were not just innocent victims, but proponents of the unfair capitalist system that led to the unrest that led to the attack - essentially, that they “deserved” it. Naturally, controversy ensued, as well as discussions on the relationship between politics and academia.

…when political matters do enter an academic setting, they must do so in academic terms.

A few years ago, a national conference was held at my university on an important topic. A flier advertising the conference went out before I saw it. One sentence in that flier began, “Now that we are fighting a racist war in Afghanistan … ” Because the flier carried with it the imprimatur of the University of Illinois at Chicago, it seemed to be the university that was issuing that judgment.

The case would have been entirely different if there had been a list of the conference’s panels on the flier, and if one of those panels had been titled, “Are We Fighting a Racist War in Afghanistan?” That would have been perfectly appropriate because it would have identified the question as one that would be debated at the conference: Speakers would give their answers and back up what they said with evidence, and other speakers would give opposing answers and cite alternative bodies of evidence. That’s what we do in the academic world…

In another section, the article says that Churchill’s writing was justifiable grounds for dismissal, but not because of the content of the writing itself; the dismissal (and in fact, the reason Churchill resigned) was not because of what he said, or even because of the public reaction to what he said (”I may disagree with what you say but I will defend to the death your right to say it”) but because of the effect public reaction had on Churchill’s ability to do his job. As in, people wouldn’t listen to him, he had a hard time speaking, publishing, and so forth - things that were in his job description.

Subtle distinction. Fine line. Strange interactions happen between academic and political, academic and religious, academic and social, legal… academic and despite (or because of) our effects to separate them. This is tremendously interesting, but very difficult to deal with (to make a broad, sweeping understatement).

Another great section, this one on how universities deal with controversial speakers or topics:

The idea is to inoculate the institution from criticism by multiplying the points of view represented so that no one of them seems to be endorsed or valued. The model for that strategy is to be found in those U.S. Supreme Court cases in which it was held that you couldn’t put a cross or a crèche on the courthouse steps unless you placed next to it a menorah or a Buddha or a wigwam or something. In that way, the state gets to display those symbols — and its tolerance — without taking any of them seriously. But that’s just the trouble. The academy flourishes when it takes ideas seriously…

I’ve been struggling with the concept of how to spread ideas. If you get them to a mass-producible form, it’s easy to distribute them without actually meaning it, without transforming people. On the other hand, if you work person to person, slowly and patiently… sometimes you can’t wait for things to happen that quickly, so you have to institutionalize them, suck the life out of much of it, mass-produce it and hand leaflets around. You institute rules that people follow blindly. You discourage people from taking ideas seriously because the rules have made the decisions for them already. (I know, this is a black and white view of things, incomplete, leaves out all sorts of stuff, and I don’t agree with this model myself.)

But in the face of a world where you can reach the whole world - or most of it, an increasingly large percentage of it - with one click, in the face of a world where one speech can have political, social, economical, religious, all these implications for billions of people spread through different continents - how do you teach? How do you learn? How do you create environments - universities, schools - conducive to the kind of teaching and learning and life in general you’d like the world to have?

I’m rambling vaguely now, so I’ll sign off and go for my meeting now.

Friday, March 9th, 2007 | Uncategorized | 1 Comment »

Vive la resistance

Merlin Mann writes about the book The War of Art and paraphrases a section of the book as such:

Resistance can be thought of as anything that pulls us away from doing the work we know is most important to us. It takes many forms (including procrastination, fear, distraction, and negative self-talk), but the effect is often similar: we find or permit all kinds of barriers to keep us from becoming the person we want to be, or from completing the thing we really want to make. Whether that’s being a published author, a composer, a playwright, or a painter, our impulse to create constantly battles an impulse to do something else, or to do nothing — to not upset our weirdly comfy stasis.

I’ve been feeling this pull a lot as of late. It’s led me to do things that make me simultaneously (1) ridiculously relaxed and happy and (2) screwed with respect to work I need to get done. Basically, I’m being selfish. In a way I’ve never been selfish before. In a way that puts my happiness above… whatever else I might have worked for before. See: the last two posts, which were me getting my learnin’ groove on without regard to anything else in the world. I learned a ton. I did a lot. I taught some folks stuff, I learned plenty from other people, I was ridiculously happy… and utterly ignored my assigned work for 4 hours I couldn’t afford.

It’s been great while it’s lasted, but really, it’s got to stop; I’m screwing over so many other things this way. For instance, classes. I should start doing well in them again. I’m trying to find a way to simultaneously be happy and graduate without “selling out” - there’s got to be a way to work within the (very loose!) constraints I’ve been given and not feel constrained by them.

Note to self: asking yourself what do you want? is possibly one of the most dangerous things you can do. Because sometimes you start doing them. That’s kind of scary. And kind of cool. And very hard to deal with.

Another sidenote: with regards to the traveling around the world thing, I think “ethnomethododology” is what I’m going for - I want to describe how people create the subsociety of engineering education that they live, work, and study within, in their own words.

I need some time to clear my brain, but I’m not going to get that time for another week and a half. I’m looking forward to spring break; I’m getting far away from civilization. That is to say, my mother is coming over and we’re going to a spa in the Berkshires - my first time at a spa, so I’m not sure what to expect - and I’m not going to bring my phone, I’m not going to bring any books, and I’m debating whether to bring my laptop (no internet; it’s just that sometimes I think really well when I’m typing stream-of-consciousness). My mom sleeps a lot more than I do, so during the nights it’s just going to be me. Thinking. Creating a little space.

Thursday, March 8th, 2007 | Uncategorized | 2 Comments »

Let’s talk about plasmids

I wanted to write down what Karen was telling me some weeks ago about her bio research, because when I write things down I understand them better (this tells you something about the kind of learner I am). Karen is a very good teacher because she’s so into her work that you can’t help but have some of that excitement rub off on you.

She was explaining her work on a protein that triggers cell death - and therefore is important to cancer research - and the amount of work they have to do, the methodologies they have to follow to work with living cells, that just blows my mind. That you can order custom genetic sequences - that they can pipe out short strings of bases cheap enough and fast enough to sell genes to researchers that want to buy them - I remember how much trouble I had just getting the DNA out of my cheek cells back in high school science class, and they can just up and make arbitrary sequences consistently enough to sell this as a service? (I am a terrible experimentalist. Careful, reproducible results are not my forte.)

And how she described mutating a plasmid vector was… damn. Plasmids are circular strands of DNA, so when they replicate they “unzip” into two circles of half-DNA. Floating little blocks of base material get attracted to the now-exposed “zipper-half” of these DNA circles until the entire plasmid is filled.

Imagine ripping two long pieces of velcro apart and throwing them into a pool of little pieces of velcro; when you pick the long strand of velcro up again, the fuzzy side will be covered with the wee pieces of velcro that stuck to it. Now imagine the velcro is striped red and green - there’ll be a green section of velcro, then a red one, then a green one, then a red one. And imagine that only green velcro can stick to green velcro and only red velcro can stick to red velcro. And that when the little pieces of velcro hit the long strip of velcro, they magically join together into one long strip of velcro themselves, so you end up with two identical pieces of velcro. That’s how DNA replicates.

To be more technical about it, there are really four “colors” of velcro - ATCG - and “A-velcro” and “T-velcro” stick only to each other, and “C-velcro” and “G-velcro” stick only to each other, so you really end up with one piece of velcro, and then the same pattern on the second piece of velcro but in different colors… the point is that the same information is contained.

So the way they mutate plasmids is that they take advantage of the time when the circle of plasmid-velcro is floating around the sea of little base-velcro-snippets, so to speak. And what you do is you throw in a section of velcro that has the sequence that you want it to mutate to. (This is the strand of DNA that’s “manufactured” and you buy custom-made, like I mentioned earlier) This short section of velcro exactly matches up with the sequence on the plasmid-velcro except for a short piece in the middle, which is the new sequence you want it to mutate into. And this piece of velcro floats around, it finds a plasmid half it matches up with, and the two ends of the mutant-velcro stick to the plasmid, just like in normal DNA replication. The middle part that’s mutated still hangs on, because it’s sticking on either side since the bases there match the plasmid. And the rest of the little bits and pieces of base-velcro join on, and it closes up the circle and merges into one continuous loop of velcro and voila, you have your new mutated plasmid.

Note: I don’t actually know what I’m talking about. I might be completely off about this.

Anyway, the cool thing about this protein that Karen is looking at is that it performs a similar function to some other protein - I can’t remember the names of these things - basically there are these two proteins that can hit the same “DIE NOW!” button on a cell - and they’re trying to figure out whether the two proteins help each other, compete with each other, or how do they interact when they’re pressing that “DIE DIE DIE” button. (By “pressing the die button” I mean the protein locks into a particular chemical receptor on the cell and triggers apoptosis.) So they’ve got all these experiments running trying to narrow down how these two proteins work. It’s subtle stuff; since you’ve got these two proteins that sort of do the same thing, if one stops working you might not be able to tell - the other one’s working so the person won’t get sick. But it’s very important to know how these proteins work, because it helps you understand cell death, which helps you understand why cells don’t die, which is what we call “cancer.”

That’s all. I just thought that was fantastically beautiful. Thank you, Karen. (And apologies for completely mangling your dinnertime lesson to me. I’m not very good at understanding or explaining any of this biochemical stuff yet.)

Wednesday, March 7th, 2007 | Uncategorized | No Comments »