Friday, April 12, 2013

Live like a billionaire



Sunday, April 7, 2013

Single molecule RNA FISH website

I had written an earlier blog post to answer some basic questions that people have about single molecule RNA FISH.  I think it was useful to at least some people, so I've decided to expand the idea to an entire website.  It has a series of answers to frequently asked questions about everything from basic science questions to imaging tips and the such.  And it also has links to some nice pictures from the lab!  Comments welcome.

Thinking vs. doing in science

Lately, I've been thinking some about whether it's always best to think about experiments before doing them.  I know, of course, you have to think about experiments you do on some level.  I guess I mean more big picture thinking about "well, is this experiment informative, what will I learn from this?" kinda stuff.  I know that on the face of it, every experiment should make sense, and that the abstract notion of the scientific method we learn in grade school, every experiment should be designed to test some scientific hypothesis.  But on the other hand, most of the interesting findings that we have come across did not really arise in this way.  If we really thought through those experiments rationally, I think we would have ended up with considerably more boring results.  I'm guessing a lot of people have had this experience, where a little side-experiment ends up being super interesting and turns into a whole line of work unto itself.  And sometimes it doesn't make sense, but you just do it and see what happens.

That said, it's important to know where the line is between interesting side-experiment and hopeless distraction.  Also, one of the most important skills to develop as a scientist is the ability to take the seed of something interesting and turn it into a coherent and logical argument through carefully planned and executed experiments.  But I guess what I'm saying is that it's important to let the mind wander sometimes.  A question: how do people find those seeds?  Is it luck?  Hard work?  A "nose" for good problems?  Or is it a skill that one can acquire and hone with experience?  I think that last one is actually more true than people think...

Centromeric DNA

I was just listening to a couple of interviews (1,2) about ENCODE, which were interesting (link from Jan Skotheim's cool blog).  But aside from the arguments about ENCODE, there was some talk about comparisons to the human genome project, and how the human genome project had a nice end goal, but that goal was perhaps a bit more subtle than most realize.  Specifically, they didn't sequence all of the genome, because they skipped some of the repeats and the centromeric regions.  Then, in discussing ENCODE, they talk about how one could define the entire genome as being "functional" by ENCODE's definition because DNA polymerase interacts with every base.

Anyway, I thought it was somehow weird/fun to think about the fact that we don't know the sequence of the centromeric regions, but we know that DNA polymerase gets in there and replicates it.  I don't know why this seems strange to me, but I guess I like to think about these situations where something goes through some unexplored region and comes out the other end without really revealing much about its journey.  It reminds of how we have laid down these huge transatlantic cables connecting the US to Europe (in 1858!).  They basically just put down a big wire running the entire distance.  The deep of the ocean is still largely a mystery, but these cables run right through it, with our information none the wiser for their deep-sea voyage.  Somehow, I find this cool...