"Re" Search

The last couple of days have served as a great reminder that when a problem arises with a critical part of an experiment, rarely is there a single solution. I thought that when an experiment was about to begin, all of the details were worked out, and the only tasks left were to collect data and analyze it.  Wrong. It has been said on several occasions that “once you smooth out the kinks, data collection is a breeze”. Finding the kinks is easy; it’s the solution that’s tricky.

The 300mL chamber that will be used
 to measure nitrogen fixation

One of our methods requires the use of an air-tight chamber. On the surface, it sounds like an easy task. Only once you try to actually make a chamber air tight do you realize the difficulty.  In our collaboration with Tanner Williamson, we are using chambers that have been designed especially for this experiment. These chambers hold only about 300 mL of water, which is ideal for measuring biological processes on a small amount of algae. The small chamber volume is important because the tiles that we are measuring nitrogen fixation on are barely a cubic inch in size. The added bonus of these chambers is that it has a recirculating fan that circulates the water within the chamber and mimic stream movement. The double-edged sword is that these chambers only have one opening. The chambers that were used in our work last year had two openings; however, those chambers were much larger (2 liters) which makes measuring nitrogen fixation more difficult. The benefit of having two openings comes into play when we are required to simultaneously add gas and remove water using two different ports. These new chambers posed two problems: being air-tight and only having one opening.

Deciding to address the gas-tight issue first, we attempted to cap the opening of the chamber with a rubber septum. It turns out that this is extremely hard to do, as you are essentially forcing an object against a positive pressure gradient. Even though we managed to get the septum on, the chambers were over-pressurized and some airspace remained inside the chamber. Plan B involved a simpler method. Underwater there should be no air, thus removing the problem of trapping air inside the chamber and over-pressurizing. Placing the septum over the top of the chamber while the septum and chamber are submerged creates a chamber that is free of air.

Using a chamber with only one opening has a few challenges within it. We are required to add gas and remove water at the same time for one of our methods. This technique becomes difficult to do when the only way into the chamber is through the septum at the top (about the size of a quarter). Two insertions (one for the gas, the other for the water) requires two people. We also have to insure that we are not pulling out the newly injected gas as we are removing water from the chamber. We then had to address the issue of which insertion would work best for injecting the gas. In other words, should we inject the gas at the top of the chamber or at the bottom? To answer this, we added blue food coloring to the chamber, with the fan running, and observed the flow pattern of the water. The food coloring instantly moves toward the fan and begins to dilute.  Based on this, we decided it would be most beneficial to add the gas at the top of the chamber and pull the water out from the bottom.
     Several hours of critical thinking mixed with trial and error resulted in these problems being solved. At the end of the day, it is extremely gratifying to have created a solution to a problem that at the beginning of the day seemed unfix-able.   These challenges have helped me to understand that critical thinking and creativity go hand in hand during research.