Saturday, December 19, 2009

Why biological engineering is hard.

(analogy time today, kids! Get's a doozy)

I started out my engineering career with things like a lego boat. The white body was a continuous piece of plastic, with room for gigantic nonfunctional sculpture-like towers that would sometimes crash over in the bathtub as Eric and I both kneeled on bath mats to have battles (that was after we almost flooded the sinks, of course). From there, I went on to houses. At first, I was all over the place in terms of color, with my 2x4 in random patterns, or in straight up and down towers that just kind of fell over. But trial and error taught me the overlapping brick method and soon I fell in love with the thought of a dream lego house with white on the sides and red roof tiles. And the flowers! Can't forget them. Ohhhh no.

from here

As my ability to judge space, height, and practice sound building principles, my homes improved. And got really good, actually. By the time Eric and I were in late elementary school, we had a huge house that spanned floors, had a hacked bathroom, and a big screen TV. I was proud of my houses...although most of the lego building I do nowadays is Star Wars ships with my other brother. Following directions and understanding how things fit together are key. That's how you succeed. That's how things work. You get a functional outcome based on these known principles.

In the same way, a field like civil engineering finds itself building bridges, fixing roads, and planning urban centers. The properties of materials like concrete, wood, and metal are known...the spaces in which they build are precisely measured and there is visual feedback through the use of levels, tape measures, and all sorts of other equipment. Processes are almost modular; no matter where you pour concrete, 98% of the time your instructions will be the same and almost immutable to any sort of variable you throw at it (this is what engineers call robustness - the ability of a system to withstand perturbation and "noise")

Biological engineering is the same. But we're still really at the lego boat falling over stage. Sometimes, success is luck. Sometimes it's like that moment where the lightbulb goes on over your head and you finally understand something that has been eluding you. Sometimes, you're able to bring things from another part of science into your arena and make it your own. But sometimes it's even's like someone set you in a room blindfolded without the lights on. There's a table covered with legos, but they're also covering the floor (and you're definitely barefoot). You can use some of your senses to come up with something that maybe looks like a house (maybe) but the colors won't be coordinated, you won't have used the most suitable pieces to create the house, you probably stubbed your toe and fell because the lights were out, and it just may fall apart. Frustrating, to be sure.

In bioengineering, we aren't at the stage where you can just turn on the lights and measure things with rulers, understand the innate properties of materials, or really see things all that clearly. You can't see all cellular interactions going on with the naked eye, you can't see how things are working internally. Granted, there are a lot of technologies being developed to help biologists really see what is going on (mass spectrometry, crystallography, NMR spectroscopy, atomic force microscopy, and a whole alphabet soup of other things). Yet, there is no way to "really" know what's going on in biology. All or our tests are proxies for things we can't actually see or measure, and this can mean that things get really complicated really fast. That's one of the reasons why this project has been so hard. Building a functioning FRET protein is exceptionally think "oh, just put one on each end, and it'll work!"

Ha. What a lie.

Building a FRET protein is like putting two pieces onto a movable sculpture but without being to see the sculpture, knowing what "glue" you're using, understanding how the sculpture will move, and having no ability to know if it actually works. Add that to the fact that this sculpture is incredibly tiny, and you're done. I could have gotten lucky. But I didn't. Which is why I'm now doing something else.

Sometimes I wish all I could do is build legos again.

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