Saturday, August 18, 2012

They're Called "Instruments" Not "Machines"

Junior Year

Adventures in Environmental BioChemistry


My next major project as an engineering student began, coincidentally, one year after the week my sensor buoy group was formed.

The disparity between my junior year spring project and the buoy reflects the broad spectrum of expertise an Environmental Engineer is expected to grasp. The subject was environmental biochemistry, a class split between intense lectures (of the old-school-cold-calling style) and lab experiments (of the don't-let-these-incompetent-undergrads-die style). Both the lectures and the lab coalesced in the final three weeks as the students were instructed to find partners, design an experiment suitable to the class material, and implement it with whatever time remained in the semester.

I was incredibly lucky to be paired with a classmate who I was used to working with. We had done problem sets and smaller projects together because we took a similar approach to work that eschewed procrastination (the fact that the two of us lived in the same building was simply a perk). 

Neither of us was particularly interested in the biology portion of biochemistry; one lab class spent waiting for bacteria to grow was as much experience with microbes as we cared to get. So we decided to focus on the chemistry aspect, reasoning that it would take less time and generally be less of a hassle (no dependence on living organisms! Yay!).

This assumption turned out to be a little presumptuous.

Defining the Experiment


The first hurdle was getting an experimental design passed our professor. He was meant to be a "sponsor" (read: sanity check) of our final project. Being the opposite of procrastinators, we bombarded him with ideas as early as possible in the project. We brainstormed and conducted literature research for feasibility analysis, then presented the project topics to our chosen professor as soon as they took shape.

It was, oddly enough, a tug-of-war between feasibility and scientific interest. Given time and budget constraints, we needed to use the resources and environment close to our campus. However, we also wanted a reasonably engaging research question. Thus my partner and I discarded ideas we considered unfeasible; our sponsor nixed anything not scientifically intriguing.

It probably should have been the other way around, but our sponsor was rather excitable. And by junior year my partner and I were wary of taking on too much work for any given project (lessons learned from the sensor buoy, perhaps).

After numerous, long discussions with our sponsor, we finally settled on a project to test the concentration of DDT in the Charles River. You know, that chemical made famous by Rachel Carson in "Silent Spring." I could give you a picture of the chemical structure here, but I doubt it would be particularly enlightening. And if you're reading this, I am confident in your ability to utilize Google.

The main motivation behind the project was a combination of the lack of published measurements of DDT since the 1980s and various articles since then claiming that there was some DDT present in the Charles. Furthermore, during our literature search we came across reports on high DDT concentrations in the lower regions of the Mystic River, not too far north from Boston.

DDT, as an organic compound, is naturally hydrophobic. However, the possibility remained that DDT was concentrated in the sediment of the river with the potential to be suspended in the water column as the sediment was disturbed.

Simplistic diagram of the flux of DDT from sediment to river water. By testing both, we could get an understanding of its concentration in the water column and the correct direction of this flux.

It seemed reasonable to update the testing for DDT in the Charles River and settle fears of its presence once and for all. The key word there, of course, is "seemed." (Ah, foreshadowing).

Collecting Samples

It was early one Thursday morning in late April. Other groups were in the student lab, just beginning to set up their experiments and think about collecting data. Professors and one lab tech were on hand to prevent us undergrads from accidentally setting the lab on fire (or something).

 My partner and I, on the other hand, were out in a small motor boat on the Charles River dunking bottles into the surface water and a grab sampler into the sediment below.

It was our first experience at fieldwork, and and a relatively nice introduction. We had sterilized jars for sediments and old chemical bottles for surface water samples. We hijacked our sponsor to drive us and the bottles to the Sailing Pavilion on the river. We had already begged the Pavilion staff to take us out that morning, and to their credit they agreed. 

(Note: boathouse staffers are just about the best people ever. If you're a scientist or engineer working with water, they are your friends when it comes to sample collection).

The work was not too complicated; for various scientific reasons (reproducibility, breadth, flux calculations) we took several samples at three locations between two bridges in the river, steering clear of the bridges themselves. The samples were from both sediment and surface water, and each one had its own quirk. The sediment was, disturbingly enough, the consistency of toothpaste, completely black, and pungent (of the anoxic variety). The water was basically cold (I had the pleasure of holding the 6 L bottles underwater until they were full, and my hands were happily numb by the end).

Sample locations, taken before and after sampling. Notice anything strange about that last location (in green)?
After a couple hours of hard work, we got all of our samples out of the river and back to the lab. It was time to figure out what, if any, DDT they possessed.

Sediment samples were put in glass jars (left) and covered in foil to stop photosynthetic activity. Water samples were put in jugs (right) which were thankfully already light-proof.

The Chemistry

Our experimental design was slightly unusual at the suggestion of our sponsor. His lab had begun to use polyethelene strips to extract organic chemicals from field samples (the idea being that organic chemicals were more attracted to this material than the sample material, be it soil or water). It was a great way, in theory, to concentrate the chemicals onto a small strip of plastic which could then be worked on in a lab.

Of course, there was a lot of extrapolating and concentration conversions behind this method. But I won't go into those; they aren't that difficult to reproduce, and my lab notebook is somewhere else at the moment.

We put polyethelene strips in each sample and left them for about a week in a tumbler (a plastic container lined with foam, suspended between to two wood sheets and spinning slowly with the help of a motor; truly an invention of necessity). The timing was unfortunately short; we would have rather kept the samples and the strips together for longer to ensure their equilibration, but the end of the semester was coming fast and luxuries like time were fleeting dreams.

After a week, then, we removed the strips from our samples and extracted them with hexane. All of this went rather smoothly; labeling and cataloging samples is a rather relaxing task.

And then it came time to analyze the extracted chemicals.

Troubles with a GC/ECD

Our analytical method of choice was a massive, old Gas Chromatography Electron Capture Detector (GC/ECD) machine. I mean instrument. I mean infuriating fossil of an instrument.

In short, it did not work. At least, not well and not often. To my chagrin, I was not allowed in the lab to do sample analysis except when either a professor or lab technician were present. This meant that I was not allowed to work outside of normal work hours, because it was highly unlikely any professor would be awake at 2 am. 

Nor was I allowed to simply work with the GC/ECD until I figured it out. There was an understandable fear from the lab techs that I, as an undergraduate, would break the machine (er, instrument) if I played with it too much. Unfortunately, this meant that I was entirely dependent on the lab techs to troubleshoot the instrument when things went wrong.

Things went wrong a lot.

The basic idea was that we had prepared standards of known DDT concentrations (as well as its breakdown products DDE and DDD) to run on the machine as a calibration. Once we had these standards measured, we could run our samples and move on to analyzing the data. 

Elution times of our DDD, DDE, and DDT standards. We had to test a wide range of concentrations and isotopes of these compounds to ensure we were testing for all possible forms of DDT.
However, the GC/ECD refused to return anything reasonable for our standards. The problem appeared to be a combination of the type of coil it used to analyze our particular range of organic compounds, the cleanliness of its interior, and its impressive age. Unfortunately, we could only fix two of the three.

So the last couple of weeks of term saw me and my partner in lab as much as we could be, only breaking to attend other classes in any given day. We spent all of this time troubleshooting the machine with the lab technician--and getting lectured by him as to why we should refer to it as an "instrument". Apparently it is a sign of respect and makes your experiment more likely to succeed.

I'm not sure how much I believe this, given that even once we began calling the ECD an "instrument" it still stubbornly refused to work. Maybe "temper tantrum" would have been a better label.

The lab tech, however, was a wonderful human being who stayed with us in the lab from early morning to evening. And with his ministrations, the instrument slowly emerged from its tantrum and began giving us actual results.

The End

With maybe four days to go, we finally had acquired data on our samples. What we did with this data is not particularly important, as there wasn't time for much processing and what we did manage to collect was rather sparse. So I will simply state the results of the experiment and leave it at that.

We found, to no one's surprise, that DDT is not at high enough concentration in the Charles River for anyone to be concerned. Its breakdown products, DDD and DDE, are present at low concentrations. Again, however, their levels are not significant enough to worry any casual swimmer or fisher in the river. They were in rather unexpected locations, however. DDD, the anoxic breakdown product, was in the surface water at higher concentrations than DDE, the oxic breakdown product. And the reverse was true for the sediment.

I am still puzzling that one out in my head, but without samples from farther upstream there is no way of knowing for sure why this counter-intuitive result exists.

And I've moved on to larger bodies of water since then, so I am not sure that I will ever return to the Charles to take the necessary measurements. The application of our experiment, after all, turned out to be rather slim. However, as an introduction to fieldwork and the tricky business of getting lab instruments to do as I please, this was a fine project.

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