Riders on the storm

Wow, here’s somebody who totally nails it:

http://www.upworthy.com/this-guy-says-were-all-faking-each-other-out-and-thats-not-helping-anything-lets-stop-that?c=ufb1

Most of the time, when we are in lab or in the field taking measurements, we are running into walls and troubleshooting ways to get through/around the walls.  It isn’t the same as ‘not knowing what we are doing’–don’t get me wrong, we are quite clear that we are testing a particular hypothesis.  Being ‘in the cloud’ as described in the video is more about running into barriers because of forgetting to examine an assumption closely, or neglecting to step back and take in the larger picture.  Science *isn’t* the shortest distance between hypothesis and results; it’s construction of testable hypotheses and the subsequent attempts to test these hypotheses based on what you think you know.  Sometimes this is pretty nonlinear.  The cloud is a scary place and it’s important but hard to keep your mind open when the lightning is flashing and you are being clobbered with hail, especially when the ‘visit’ to the cloud stretches for months or years. 

Good example of being ‘in the cloud’:

I teach a genomics class each fall (except this fall;  sabbatical).  I teach the students in the class (beginning grads and advanced undergads) the basics of molecular evolution, show them cool databases and tools to make sense of the vast amounts of data contained therein, and then have them use the tools and their understanding of molecular evolution to test hypotheses.  One year, the dataset we were using was the complete sequence of a deep-sea bacterium that I study and we hypothesized that the genes encoding the enzymes that catalyze sequential steps in pathways to build cellular building blocks like amino acids would cluster together like pearls on a string on the chromosome.  This is what we see in our pal E. coli, the best-studied bacterium on the planet.  I gave each student a biochemical pathway and told them to construct a map showing the location of the genes encoding the enzymes of each pathway.  I expected each student to hand in one map showing the genes nicely adjacent to one another (pearls on a string, right?  Easy-peasy.).  We all left for the weekend and I told the students to hand their maps in on Monday.

Soooooo.  Monday comes.  Mass pandemonium!  Shouts of mutiny!  Pearls on a string?  Get serious!  Those genes were tossed around all over the place on the chromosome like a tornado had hit it.  Students came up to the front to hand in their assignment.  Instead of a single map each, they staggered under thick stacks of maps showing how gene A was on top of a tree, while gene B was over in the cow pen by the lake (tornado metaphor alert).  The students were furious.

I apologized profusely, and then paused, and realized this was way cool.  We started asking WHY the genes were so disorganized, and came up with a different way to think about why genes might not act like pearls on a string (sorry, it doesn’t involve tornadoes).  We put it into a manuscript which got published by a fancy journal, and our new idea gets cited quite a bit.

(That author line is so long because the students are on it.  That insane weekend assignment paid off in the end.)

tcru genome

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