I’m fully immersed in writing a big grant proposal so I have even less time for blogging and reading blogs than usual, but that doesn’t mean I have no time. Along with my colleagues I’ve been working on this beast for 9 months, but now with only 3 months to go before the deadline it’s crunch time (the last time we did a competitive renewal of this thing the application was over 900 pages long and this one will be close to that). So time is a precious commodity.
It is also a fascinating biological variable and scienceblogs is blessed with several experts on the subject, notably Coturnix at Blog Around the Clock. We also have a new colleague on scienceblogs, Harvard PhD candidate Christina Agapakis who works on synthetic biology and blogs about it on her new blog (new to scienceblogs site but she is an experienced blogger), Oscillator. It’s always nice to extend a welcome to new sciblings on principle but in this case I thought about her specifically when I ran across a nifty video from Nature on a new paper from some synthetic biologists at UCSD showing it is possible to synchronize the internal clocks of the common lab enteric bacterium E. coli. These internal clocks are just oscillators so I figured Christina would have blogged about it and indeed she had, complete with a video and a short note with links explaining key biological clock terms. It turns out that her video and mine are different, however, which gives me an excuse to put it here without duplicating her fine post.
The science of biological oscillators is fascinating but so is the mathematics. Lots of physical systems have “natural frequencies,” the most well known being the simple pendulum whose back and forth swings are governed only by its length (I am ignoring large angle swings which make a small difference). Our legs are like pendula swinging from our hip which means that if we were to stand on one foot and extend our leg backwards a bit and then let it go it would swing back and forth with a natural frequency approximately the same was our natural walking gait. If we want to swing our leg faster or slower than that natural frequency we have to force the pendulum by using muscles. A pendulum is a linear oscillator but there are non-linear oscillators, too, and they can have interesting periodic behavior that is less symmetrical than a simple pendulum’s. And even more interesting things happen when you couple pendula, for example hanging another pendulum from the tip of a first one and watching the behavior of the tip of the bottom one.
The problem with individual oscillators is that they aren’t inherently synchronized. The new Nature paper actually constructs within living E. coli a genetically engineered oscillator and uses a communication process called quorum sensing to synchronize them. The video below explains some of this. Go to Christina’s blog for more information about oscillators and other working models of living things (synthetic biology) and you can read this News and Views explanation of the paper in Nature has a lot of technical details on the paper and synthetic E. coli oscillators.
To whet your appetite, here’s the video from Nature: