May 22, 2008

How to Levitate a Biologist or Zen and the Art of Alignment

Every day is a learning experience. Today, I learned that I can fly. I don't need an airplane and I don't need a helicopter. All I need is Macclade.

I'll assume that most of the people who read this note will never have done an alignment. It's a very meditative thing, really. One can download a bunch of sequences from GenBank for starters. Make a list of the sequences you want to download, save them as text files, clean them up, load them into Clustal (personally, I like W2 best) to generate an initial alignment, then load that initial alignment onto Macclade to fix it up. That's where the really meditative part begins. One slides colorful little blocks around to line up bases, deciding where gaps should go and what characters constitute insertions and deletions. It's very Zen, this business of alignment. The more dissimilar the sequences are the longer it takes and the more I concentrate on the task at hand to the exclusion of everything else in my environment.

And this is why all I need to fly is Macclade and a little help, which comes in the form of one of my lablings walking up quietly behind me, peering over my shoulder at the screen and asking loudly, "You believe in this stuff? All those little A's and T's?"


I'm suddenly six inches above the seat of my chair. My hand has convulsed and selected four taxa which slide themselves to the top of the screen. My cytochrome oxidase subunit 1 alignment, so neatly lined up over the course of an hour, suddenly looks like red, green, blue and yellow swiss cheese. Thank Maddison that Macclade has an "undo" button.

Years ago, Maharishi Mahesh Yogi conned his followers into thinking that they could learn how to levitate based on spiritual principles. As usual, it takes science to actually get a man off the ground.

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