Day 27 - The Countdown

Photo credit: http://libraries.mit.edu/esl/barker/about-barker.html

One more day of the experiment, and the trends I see are tiny. I plotted the data from my fluorometer measurements, and all of the compounds started out at around the same number of fluorescent units, which was a good sign. By the third day, they've all increased at close to the same rate, but the algae in ibuprofen seem to be doing the best. Caffeine appears to be the most harmful to the algae so far, but the differences are limited.

Today I went to the Barker Engineering Library for the first time. When I stepped off the elevator on the 5th floor, I was surprised and almost dismayed by the cramped space and low ceilings. But when I turned a corner cautiously, I found myself inside the great dome of MIT. I stopped and gazed up at the intricate patterns of the dome and the giant, silent hall before me. The room was completely silent, although there were quite a few students inside. The desks were set up as little triangular booths that offered much privacy. Each booth had a personal desk light, a comfortable chair, and a semicircular desk surface that I soon found was an ingenious design for studying. Although the desk occupied very little space, the desk surface felt long and spacious because it almost wrapped around the studier. The environment of Barker really does inspire and promote studious behaviour! I wish I had discovered it earlier.

Day 26 - Fluorometer and report

For the entire weekend, I could not stop worrying about the algae. I could not keep the fan on, so I was afraid that the algae would be overheated. What if a bottle tipped over and knocked down several other bottles with it? I ran in this morning, flung the aluminum foil aside, and...breathed out in relief. The algae were doing fine, and they were much greener than they were last Friday. I had tried installing an air pump and airstones, but half of the airlines did not work. The ones that did produced very inconsistent bubbles. It would only take away from the control of my experiment, so I decided to circulate the algae by shaking the bottles a few times every day. I am also randomizing the bottles by switching their positions so that they would receive equal amounts of UV light.

I worked on my presentation and paper in the library in the afternoon. At around 4:00, I transferred 20 mL of each solution into their corresponding plastic containers and took them all to Parsons with Julie. We again measured the chlorophyll concentrations in the fluorometer. This time they were significantly higher - on the order of 10-17 fluorescent units. However, I am concerned that the results displayed too much variety. Also, all four bottles in the third set of the triplicate exhibited consistently low chlorophyll levels. My theory is that I happened to place all of the bottles of the third set towards the sides of the tank over the weekend, so they may have received less light. I hope that I will see some distinct growth curves by Wednesday.

Days 24 & 25 - Algae developments

On Thursday, two of Sarah's interns at the MEC gave presentations about their work on algae biodiesel. The first intern had helped to create a biodiesel reactor, which combined waste vegetable oil and algae oil in a water heater. Currently, much research is being done on the most efficient method of extracting oil from the algae. The second intern and Sarah have been trying different methods of harvesting algae and extracting oil - centrifugation, filtration, alcohol, etc. All three of them have been working on taking apart the old aquaculture exhibits and replacing them with algae biodiesel exhibits. They are going to build their own photobioreactor for the algae once the materials arrive, and one of the interns is working on a see-through exhibit that shows the step-by-step process for biodiesel production. They are also developing a thick book titled "Home-Brew Biodiesel."

It was especially relevant for me to hear their talk on algae biodiesel. I am only focusing on a tiny slice of research - cultivation and nutrient removal from wastewater. In the future, I hope to venture into the other stages of biodiesel production, such as lipid removal, cell harvest, and perhaps even the economics of biodiesel.

After the presentation, Sarah and the two interns visited my humble algae culture in the back room. Sarah advised me to double the nutrient content and allow the algae 24-hour light cycles. At her suggestion, I also set up a fan to prevent overheating.

On Friday, I saw some improvements in the starter cultures. I was in the library working on my report when Julie informed me that Ms. Frankel at Parsons Lab has a fluorometer that I might be able to use to measure chlorophyll content. This would be a more accurate way of quantifying the algae growth. I hurried excitedly back to Sea Grant, checked in with Julie, and quickly pipetted 10 mL of my starter culture to each of the PPCP solutions (w/ 1 mL of nutrient solution). I was running out of time, because Ms. Frankel had to leave no later than 5:00. Quickly, but as accurately as possible, I poured 10 mL of each solution (with the newly added algae) into labeled plastic tubes and carried them in a brown bag over to Parsons.

Julie and Ms. Frankel were waiting for me there with a huge, antique field instrument -- the fluorometer -- that measures chlorophyll content. With Julie's help, we poured each of the solutions into small glass tubes and inserted them into the fluorometer. The calibrated fluorometer then gave a reading of the chlorophyll content, which I recorded in a data table. To my relief, all of the concentrations came out relatively similar. All of the solutions ranged from around 0.6 to 0.65 fluorescent units. On Monday, Tuesday, and Wednesday, I will take chlorophyll measurements again and hope to see variations among the PPCPs.

Day 23 - Portsmouth Naval Shipyard

"No phones allowed, no cameras...hard hats and CIA badges must be worn at all times."

This is what we were told this morning as we entered the gates of the Portsmouth Naval Shipyard. Matt had rented a Zipcar and drove all four of us to Maine for this top-secret tour of the shipyard. Our escorts, Rick and Nancy, picked us up in a black van and drove us to their central office. Both were very friendly and gave us a presentation on engineering careers with the Navy. Portsmouth alone employs over 1400 engineers in nearly all fields of engineering. The Portsmouth Shipyard specializes in submarine maintenance and repair; subs from around the world are shipped to Portsmouth for repairs or even complete overhauls. Portsmouth also sends some squads out to rescue subs. Rick actually worked in rescue for years. He described a special suit that submarine operators would step into, and as they breathed out, they would float up to the surface, avoiding the bends.

The shipyard is like a city in itself. There are barracks, many massive machine shops, a chapel, a day care, a school, a tavern, a post office, fitness center, and more. Rick and Nancy took us on a very efficient tour. Our first stop was the materials testing labs, where they test the resistance of rubbers and metals to see if they meet regulations. We observed a machine stretching a piece of metal, saw the metal thin out gradually in the middle, and jumped as...BANG!...the metal broke in two.

We stopped by the weld shop, which contains massive welders and machines of an unimaginable scale. I had no idea that submarines could be so huge. The building itself probably spanned several acres and is tall enough to fit several heavy-lifting cranes. The weld shop was loud, with bright lights and sparks flying from many of the welders. There was a specially-designed machine to weld batteries and a brace to remove the entire front part of a submarine. I thought the weld shop was daunting, but I never imagined that the parts shop would be even more massive. As we entered, a huge hook crane attached to the ceiling slid past directly above our heads, causing me to duck automatically, though it was hundreds of feet above us. This machine shop was like a factory; it could make pretty much any metal part one might think of. The machinists followed orders and designs from engineers. There were machines that could cut, drill and shape parts weighing thousands of pounds from a simple piece of sheet metal. We touched a raindrop-shaped piece that was responsible for driving the ship underwater or angling it back up again. We witnessed real propeller shafts that spanned nearly across the width of factory and were held and spun by even larger props.

After this, we visited the motor/electric shop, where engineers overhauled submarine motors. First, they would remove a motor from a submarine or ship and wash it. Next, they would bake it in an oven to dry, then test the quality of the motor to determine what repairs are necessary. Sometimes they would replace all the metal bars on the rotating part of the motor, then dip it in a type of glaze for protection. Once glazed, the motors actually looked beautiful, like old lacquer furniture with a striped design.

We passed a submarine docking area that they were renovating. It's size reminded me of a lagoon or a channel. They built a number of platforms several stories high that they would attach to the sides of a docking submarine so that they can easily climb inside and get around without even having to step outside. We were lucky enough to see DSV-4 Sea Cliff, the sister ship to the Alvin and Turtle. Owned by the Navy, the Sea Cliff was retired from service in 1998. It was a 3-person research vessel that could dive up to 20,000 feet. They now keep the DSV-4 it in a storage warehouse, because some of the parts on it are potentially useful in other crafts. I wish I could go for a ride in a submarine someday. The shipyard staff were actually trying to recruit us to work for the Navy as engineers. It's something to think about for the future!

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Back at Sea Grant in the afternoon, I had to dump out all 15 bottles of tap water that I sterilized and re-sterilize 15 bottles of spring water. The starter cultures that I grew in tap water over the weekend did not fare very well, but the cultures that I grew in spring water on Monday are starting to look faintly green...

Day 22 - MIT museum

After a few wrong turns and rounds of walking in circles, Cole and I made it to the MIT museum. Kurt, the marine curator, gave us a personal tour of the museum. He showed us the first floor, which contains 7 mini exhibits on MIT innovations and research. There are some researchers who are trying to develop batteriess out of viruses! Another exhibit featured a tiny tank of copepods, and we got to turn a wheel to capture photos of slices of the tank. Then, we could zoom in on a certain area and adjust the resolution to oberve the copepods shapes.

Upstairs there were robots and robot parts that were decades old. There was another section of the museum that showed high-tech, moving art. My favorite was a violin with a feather duster sliding tenderly back and forth over it. Another contraption composed of several consecutive wheels apparently takes several billion years to turn a stone block at the end. It is meant to represent infinity.

The holograms were the best part of the museum by far. Holography may best be described as 3-D photography that appears to move as the viewer changes orientation. It reminded me of the animated photographs and portraits in Harry Potter. A hologram is constructed from the light scattered from an object.
Photo credit: http://web.mit.edu/museum/exhibitions/holography.html


Kurt then took us back into their storage rooms. He showed us map prints and lithographs from the 1700s and 1800s. The level of detail achieved by the metal reliefs from hundreds of years ago baffles me. Ship captains were able to study the maps and follow lines drawn over the ocean to navigate to their destinations. Kurt also showed us a reconstructed ROV that could contain the original body of Jason, the ROV that went down to the Titanic (Jason had a twin).


I plan to revisit the MIT museum next week to go through all of the exhibits that we skipped during the tour!

Day 21 - Grow, algae, grow!

The algae starter cultures aren't growing! The water in the two bottles looks as clear as it did on Friday. Julie hypothesized that it might be because they were grown in tap water. I sterilized some spring water and made two more starter cultures with the double the amount of F/2 nutrient medium. I put the new cultures under the UV lamps, so hopefully they will grow more quickly. Today I also set up the air pumps and cut tubing for 15 airlines. I hope to be able to put the algae into the PPCP solutions soon. I hope to see green tomorrow!

Cole and I lugged around water quality testing tools, a Sea Perch, a massive heavy battery, and a camera to the sailing pavilion (which we found closed) and then to the public access dock. When we got everything set up in the stifling heat, we found that the camera had run out of battery, so had to run back to Sea Grant and switch cameras. We finally managed to film a dramatic scene of the Sea Perch (my Kraken) being lowered into the depths far below and a hero scientist saving the Sea Perch from the hungry Giant Squid. Once I hauled in the Kraken and collected a water sample, we demonstrated use of a refractometer. Tomorrow we will be filming other water quality tests, such as the ammonia and nitrate/nitrite.

Day 20 - Experimental set-up

The algae arrived today! It came in to glass vials filled with agar, and it looked like streaks of green smeared on top. In the morning, I finished sterilizing about 20 L of tap water by boiling it in a kettle. I poured 400 mL into each of the 21 half-liter bottles.

For the experimental set-up, I covered a tank with foil on all sides to provide the algae with ambient lighting. Matt spent much of the day helping me build a stand for the UV lights and wiring the lights. Thanks to Matt, I simply plug in a cord, and the algae will have the bright light they need for optimum growth.

I scraped some algae off from the agar and transferred it to two starter culture bottles with some growth medium in each.

I am also much indebted to Julie, who talked me through every step and walked over to Parsons to grind and weigh out the caffeine and ibuprofen pills. I used pipettes to measure out the needed volumes of DEET and antibacterial soap. All the chemicals were deposited into stock solutions, which will be transferred to the other 15 bottles with the algae once the algae have time to grow over the weekend.