Garrett (garote) wrote,
Garrett
garote

Day three.

My brain is bursting with crazy-ass amounts of information!

Third day of work: This time the bike ride went even smoother. I still had trouble locating space to lock my recumbent, but that's a minor annoyance. I trooped upstairs with my saddlebags, stowed them under my desk, and went to the bathroom to change into my "work clothes". This trek is amusing because it involves cutting through a lab storage area, so I need to put on big plastic goggles for 15 seconds and remove them once I reach the other door, and repeat the process when I come back.

I sat down at my desk for about 30 seconds, then Hector came over and walked me across the building to his cubicle, where he gave me a 45-minute personal presentation, jumping from one slide show to the next as the subject changed in the conversation. He explained the JBEI's objectives, and the state of the research environment. One of the things he showed me was a chart on a piece of paper, made of hundreds of lines and arrows connecting little bits of text, in graceful curving lines.

Each piece of text was annotated by a cluster of icons and colored symbols. There was an almost overwhelming amount of information packed into it. The chart, Hector explained, was a map of all the known metabolic pathways in a single tiny organism, with references back to the actual pieces of the organism's genome that were responsible for each step along the path.

Essentially, each piece of text represented a variety of molecule, and each arrow represented a conversion from one molecule into another. Every conversion was triggered, or facilitated, by a protein catalyst, that was transcribed from some known and documented part - or parts - of the genome of the organism.

To me, it looked like the circuit diagram inside a microchip. It was easy to imagine a little roadmap like this inside every cell of an organism, including the cells inside my own body, and in a way that idea was accurate, but in another way it completely failed to describe what really goes on. Each of the steps on this labeled map of pathways is actually happening all at once, all together, crammed inside the three-dimensional volume of a cell like a blizzard in a snow-globe.

Perhaps a better way to imagine it would be like cooking popcorn. You have unpopped kernels and popped ones - call them U and P - and at first you start out with all the kernels unpopped - 100% U - and by applying heat you convert them all to popped ones - P. You could describe this as a pathway, by drawing an arrow between U and P on a piece of paper. Looks pretty simple if you draw it that way. But what is really going on, when you put the popcorn in the microwave? The kernels are going "bang!", one at a time, in random places all over the bag. It's a crazy, complicated phenomenon happening in 3D space.

Now imagine that the bag is the size of a football stadium. And now imagine that instead of one kind of popcorn, it's filled with one thousand different kinds, all popping at once.

Now imagine that instead of the kernels popping, they actually change into different varieties of popcorn instead.

That's about what it's like inside every cell of our bodies. The input for this thunderous conflagration would be heat, in the case of popcorn. Inside a cell, the input is oxygen, and electrons. A controlled burn.

So anyway, I got a huge brain-ful of this, and the various methods they used to refine the metabolic charts - radioactive carbon tagging, for example - and then I got an overview of all the software pieces that various departments were working on to facilitate this research.

My head was practically spinning by the end of the hour.

I returned to my desk, and sat down and poked at code in my piece of the project for about an hour and a half, then Hector came by again and walked me across the street to another lab, affiliated with the JBEI, and introduced me to eight more people, who were all working on a huge software project called "kbase".

I talked for almost an hour with those guys, getting an idea for how my project integrated with theirs, and where it might go in the future. Kbase is apparently an attempt to create a consolidated repository for all the data and methods being generated by different research facilities worldwide. An attempt to unify data in Genomics, Proteomics, Transcriptomics, Metabolomics, and Exomics. The project is related to JBEI the same way a librarian is related to a non-fiction writer.

Based on those conversations, in a few weeks I may end up redesigning, or completely scrapping, the project I'm working on - a sub-component called the Growth Curve Data Measurement System - and integrating it into either Kbase or GLAMM. I may even move next-door to merge with the programming team there. We'll see!

In the meantime, I'm re-architecting some of the bits of my project that were not coded very well. Today I stayed almost two hours late to finish a rewrite of the authentication scheme, disentangling it from the Javascript user interface code.

Two days from now is my first meeting, and if I'm lucky, I'll have a modified prototype to show off. It'll represent proof that I can really walk the walk.

And now it's time to switch the laundry!! Then, I shall hurl myself into the bed.

I'm a bit surprised at myself. I'd barely written a single line of code since last July - nine months ago - but for the past three days I have been cranking it out. It feels like my brain has gone from 30mph to 130mph, all at once, and it is a great relief to know I still have my talents.

Now comes the challenge of pacing. This is not some week-long mini-project. This is an entire organization, and a years' worth of work, in a relentless march of eight-hour chunks. It will not stop. So, getting adequate rest, adequate food, good exercise, and meaningful leisure time is as important as ever. Important as it was five years ago, when I dove into my work at Apple.

I am bringing my A-game. I refuse to bring anything less.
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