Week 7

            I just finished watching Sylvia Earle’s TED talk, which was very well done. She covered many of the problems facing our oceans today. Talks like these definitely help to give me motivation to make a difference in the field of marine science. The first point she brings up is that we used to think the oceans were inexhaustible, but of course now we know better. This reminded me of my grandmother who always tells me that the oceans are so vast humans could never damage them. It seems completely unreasonable to think that today, but I suppose this was the consensus year ago.

            The second sensor project didn’t turn out quite like Dana and I had planned. We ended up changing our sensor to a temperature sensor, because we could not get a stable reading using our fluorometer set up. We integrated our fluorometer with the microchip, but when looking at the output, the counts were jumping over a very large rang.  Then when we changed the sample to a more concentrated dilution, the change was to small to be significant. We were running low on time, so we changed to a temperature sensor. Calibrating the temperature sensor was much easier then calibrating the fluorometer. We also had much less variation in the counts then we did with the fluorometer. We averaged six readings in order to reduce the variability in the counts even more.

            We ran into a couple problems when fitting a line through our measured temperature points. The calibration curve was not linear, so we found the best fit by using a fourth degree polynomial regression line, which fit almost perfect (R^2=0.9998). However, when we took the equation excel gave us for the line and entered the count values, it consistently gave us the wrong temperature value. I did the regression analysis again in matlab and got the same equation, however this time I got the equation to a few more decimal places. Using the equation matlab generated worked much better.

            I then spent more time then I had wished trying to insert the equation into the code. I wanted to the output of the microchip to be already in degrees Celsius, not in counts. No matter how I entered the equation, it would not work. It would output numbers that were far too large (>1000). Perhaps the microchip cannot perform more then a few operations in a row. However, I expect that the chip can perform the math and I am just entering something wrong. We ended up just entering the counts into the equation in excel to find the temperature. Our sensor performed well yesterday when we had a mystery sample; it found the temperature within one degree Celsius.

            We also ended up watching the space shuttle launch at the end of last class, which was pretty exciting. I am terribly disappointed that our space program is being downsized. It may be difficult to justify spending large amounts of money on a space program, but I believe it’s a mistake to cut funding to NASA and our space program. I believe discovery unites people, and there is nothing like discovery beyond our planet to unite people around the globe. 

Week 6

            I am looking forward to intergrading our fluorometer with the microchip on the breadboard. I think we will get much better results this way, instead of using the LED readout on the RadioShack kit. I also plan on putting our entire fluorometer set up in a box next week. This way we can keep out a lot of the ambient light. You will open the top of the box to put the sample in and then close it to read the sample.

            Last night I read a few chapters in the physical computing book, which I wish I had read before last class. Last class I was a bit confused about how the microchip works and what pins correspond to what. However, after reading the book I think I have a good understanding of how it works. I also read a bit about the BASIC programming language, it seems pretty strait forward and should not be hard to work with.

            My understanding of circuits and how electronics work is also coming together. For example I did not understand how components in a circuit could be controlled by a microchip. After doing the simple set up with the microchip and the LED last class, I realize the microchip can control the current sent to the LED and thus regulate the flashes. The example that we did last class tells me that the microchip also has some way of measuring time, which was alluded to in one of the chapter in the book.

            In the future I need to make sure I know the function of every pin on every component, this will greatly enhance my understanding of the circuits I build. One of my goals in this class is to be able to build circuits without instructions. I want to be able to build circuits just based on my knowledge of the components. 

Week 5

            I have chosen to go ahead with the fluorometer for my sensor. I am working with Dana on the sensor and we have made good progress this week. We started out by building a light detector using the photo resistor provided in the RadioShack kit. The circuit design was very simple and is connected to a potentiometer so we can adjust the sensitivity. The light intensity is displayed on the led readout on the RadioShack kit. That was the easy part.

            Next we set up a system of clamps so we can arrange a place for our light source, photo resistor, and our sample. We used a small test tube to hold our sample and a blue led light from the lab as the light source. We narrowed the beam of the light by pointing it at a small aperture. Our sample is located behind the aperture where the restricted beam of light will hit it. Perpendicular to the blue beam of light is our photo resistor. It is placed about a centimeter away from the sample. Over the photo resistor we have placed five layers of thin red transparent plastic. This stops the majority of scattered blue light from entering the photo resistor.

            The third step was obtaining a sample of known concentration to calibrate the fluorometer. This did not go so well, because we could not find any fluorometer to measure a sample. Neither Jim nor Bob Kirk (head of the chemistry laboratories) knew of a fluorometer we could use. So we decided to make a stock solution of unknown chlorophyll concentration and make our calibration in reference to this stock solution. We did this by using a quick and dirty chlorophyll extraction procedure. We boiled a few spinach leaves then mashed them into a paste and allowed the paste to sit overnight in rubbing alcohol. The next day we sieved the remaining chunks of spinach out of the mixture. It worked very well, the solution lights up bright red under blue light.

            We then started making dilutions of this stock solution in rubbing alcohol. We tried MANY different dilutions but did not find any correlation between concentration and the led readout. The next day we rearranged our set up and made sure every piece of the layout was very steady. Most importantly we made a new holder for the samples, so the samples would be in exactly the same position every time. We finally found good results by making dilutions using only drops from the stock solutions in six milliliters of rubbing alcohol. We blanked our fluorometer system by putting in a sample of only rubbing alcohol and adjusting the potentiometer so the led readout was zero. We increased the concentration by five-drop intervals until we reached 55 drops and the led readout was 10. We made a calibration curve from these measurements. Our curve is linear from 0 to 20 drops, and then follows another linear trend with a lesser slope from 20 to 55 drops. I don’t quite understand this, but it seems to work.

            I hope everything works for us on Tuesday although I am a little worried. We really struggled with making a calibration curve for our fluorometer because our results were not consistent. Also I am not sure how much our stock solution of chlorophyll will degrade over the weekend. Perhaps on Tuesday our stock solution will have lost some of its chlorophyll content. As of now it is in a jar in my fridge and I have my fingers crossed. Overall, I had fun making it and even more fun watching different solutions fluoresce under blue light. The picture below is our fluorometer while a sample is being read.

Week 4

            The talk by Bonnie Bassler was very thought provoking. What I liked the best was the connection she made between intercellular communication and multicellular organisms. It makes perfect sense that this would lead to multicellular organisms, because the cells inside multicellular organisms still have to communicate with each other. I also liked the introduction where she talks about the number of bacteria on a single human. The number of bacterial cells on a human is ten times that of human cells, I find that to be an impressive amount. This is a symbiotic relationship that seems to get little attention.

            I had a lot of fun building simple circuits on Thursday. The little bit of circuit building I did left me wanting to do more. I am excited to start creating my sensor, however I still have not chosen a specific sensor yet. I am considering a light sensor that will measure light intensity. Next class I want to try building a circuit only from the circuit diagram, not the step-by-step instructions in the book. One thing I am confused about is the need for so many resistors even in simple circuits. Why doesn’t a single resistor proved ample resistance? I am sure it will all make sense as I become more immersed in the subject. In any case, I can’t wait till next class.