Thursday, July 8, 2010

Summer Research Week 1

My first week:

How to begin? Whenever starting something new or different, the first action or step taken is the most difficult one. At BCH all of you have gone through an orientation process, beginning with a guided tour of the campus followed by a look at some of the possible activities and courses you might choose to become involved with: will I try out for baseball or tennis, will I get involved with the Model UN or the Key Society, or will I take Biology AP my junior or senior year. The permutations are virtually endless. It is very easy to get lost and feel overwhelmed. What can help keep that from happening is guidance from others who know how you are feeling. For many of you that help has come from a teacher, a guidance couselor, or a senior mentor. Well, when I arrived at BU the first day, I felt, as you have felt this challenge of getting to now a new place. Instead of senior mentors we were helped by faculty associated with the BU RET program. They helped get us acclimated, beginning with new photo ID cards. Boy, do I hate those. Anyway, just like you, we needed to register in order to gain access to the extraordinary range of resources that the University can provide. I would like to say that our introduction to the University's computer system went flawlessly, but when does anything with computer systems go without a hitch? Anyway, time heals all wounds even those involving semiconductors, and I look forward to when all my computer issues are resolved.
That first day as well, we were taken through a training course in lab safety. We attended the session with high school studentsjust like you from around the country who are spending their summer working in labs at BU. Very impressive. Boy, I wish that I had taken advantage of such an opportunity...perhaps some of you may consider doing such a program. In any case, I was fully prepared to find the lab safety talk a real bore. As a teacher I certainly appreciate hos critical the subject is and certainly emphasize it with all my students in lab, but I thought a talk geared to high school students would have little to offer me. I was mistaken. Not only did I pick up new information, but the presenter was able to keep all of us engaged and interested. The talk was then followed by luunch served in a room with a panoramic view of much of Boston. The chocolate cookies were to die for, almost as good as Mary Sullivan's version in our own school.
Later in the week we had a followup training in laser safety. It was an eye-opener for me as many of my misconceptions regarding lasers were put to rest. Like you, my only real experience with lasers involved the laser pointers that I have used in the classroom. I came away with a fresh appreciation of the techology behind and the caution required in the safe use of even these relatively tame applications of laser technology.
During this first week as well we had several introductory lectures regarding what photonics is all about, including a "review" of some of the basic underlying physics. Wow, what I have forgotten! My last formal course in physics was as an undergraduate, a great many years ago. Not one of my favorite courses and pursued only as a prerequisite to further study in the sciences in which I was more interested. I remember taking a course in middle school involving the works of Shakespeare and getting little out of it. Later on in life, however, it began to make sense and worked for me as my life experiences gave me a better lens through which to view his works. In some ways, reacquainting myself with both the theory and application of physics is similar. At his point in life I can now better appreciate both the inherent beauty and power of physics as a fundamental tool in better understanding and responding to the world around us. One of the lectures also involved a look at some of the ways in which photonics may be used. The variety of real and potential applications was extensive and exciting ranging from use in diagnostics, disease treatment, and industry. Cutting edge stuff that I hope some of you may ultimately pursue as you are truly limited only be your imagination and the underlying laws of physics.
During this first week I also became acquainted with the specific lab that I would be working with. An important part of the RET program involves the pairing of a more veteran teacher with a less experienced one. I have the good fortune of working with a young woman, Ashley, who has just graduated from BU and who will be beginning her teaching career this fall as a middle school science teacher. As a recent graduate and a former engineering major herself, her knowledge of the school coupled with her enthusiasm has been invaluable. It is exciting and rewarding to me to see such a talented and energetic young woman just entering the field of teaching science. Perhaps some of you may eventually consider joining Ashley and myself in the classroom and lab as well.

Next up, we met Carlos, who gave us a tour of the lab in which we would be working. Carlos is a great guy and a native of San Diego. He is a post-doc, which means that he has already earned his Ph.D and now is employed in a lab working on a given research project. Most post-docs eventually move on to professions in education or industry. It is similar to being a resident in medicine. We also sat in on our first lab meeting, were all of the members of the lab updated each other on what they were doing. Many people think of scientists as figures working alone in their labs, but just the opposite is true. Science often involves working as a team with collaboration with others an essential part of the whole process. That is one reason why science requires you to develop your skills as a communicator.

Well, those are some of the highlights from the first week of this six-week program. Just like you may have felt after your first week of school, I was both a bit overwhelmed, but even more excited about the week to follow.

My second week:

We began the week with a discussion lead by one of the BU professors centered around the best research practices. We talked about what constitutes "good" research, where to start and how to best proceed in our investigations. Lots of good ideas. This was followed the next day by our introduction to a clean room. Quite simply, some research or manufacturing activities require a space free of airborne contaminants. An operating room is one such example in which the goal is a sterile environment free of germs that could infect your patient. In a similar fashion, a clean room may be required in research so that delicate equipment is not contaminated. All of us were excited when we entered the outer room where we had to don protective jump suits, gloves and booties. The whole combination is often referred to as a 'bunny suit' for obvious reasons. Think as well how the oompah loompahs looked in the movie Willie get the picture. In our tour of the clean room we saw some of the intial steps used in creating very small diffraction gratings (think nanotechnology). These structures can be used in a wide range of imaging and diagnostic applications...more on this later.
Much of the week was spent reading about the research that was going on in our lab and thinking about questions that we might try to answer during our time here. Besides a lot of reading we met with a number of people in the lab in order to discuss our ideas with them. Based on our review of the scientific litereature and our conversations we thought that it would be fun to see whether one of the instruments that was used in their lab could be employed as a biomonitor in helping assess water quality. One of the real challenges facing many people today is access to clean drinking water. Many things can render water unsafe to drink or even bathe in. Although many bacteria can be helpful to human activities and biological processes, there are some that can make people sick, think cholera for example. if you have ever gone swimming at a public beach, the quality of that water has to be routinely monitored in order to assure that it is safe for people to use. However, the assay that is normally used does not directly test for the actual disease-causing bacteria and therefore may not really protect you from getting sick from polluted water. We thought that it would be very useful if we could demonstrate that thier system could be used to directly sample for the presence and amount of disease-causing (pathogenic) bacteria in water samples. The system that we proposed to use basically uses light
to detect accumulation of very small amounts of biologial material. A really cool design that can use a either a tunable laser as a light source or a light emitting diode (LED). Technically, the system is known as an interferometric reflectance imaging sensor or IRIS for short. The lab is currently developing an inexpensive, LED-based system that could readily be used in the field. This would be really useful for developing countries in particular, who lack the resources to inexpensively test the quality of their drinking water.
The week was capped off with a department picnic. Forget your stereotypes of engineers and scientists, these folks can party! Great food and folks made the picnic a real highlight

My third week:
Two steps forward and one step back. First, the two steps forward. We got to spend another day in the Clean Room only this time we actually began to understand what was going on. We worked with a number of different instruments as we applied a chemical (photoresist) to silicon wafers, ultimately revealing the underlying grids that had been cut the previous week. We then examined the wafers with an optical microscope that allowed us to see the pattern and details of the grid itself. As many of you have already found out, there is a real excitement when your efforts in lab result in something new being revealed to you.. We will continue working with these diffraction gratings that we have helped create next week as well.
The other step forward involved a discussion as to how we could best present information to others whether in a talk or through a poster. No matter how exciting or significant your work may be, it ultimately needs to be communicated in a form that others can understand and engage their interest as well. Our discussion provided me with a variety of insights into how I can communicate more effectively with my audience whether in the lab or the classroom. Hopefully, some of these techniques will help me in better helping you to understand the material that we are learning together.
As for the step back, the pace of the lab environment can vary tremendously with people sometimes working feverishly, but punctuated by periods in which the pace of your tasks changes significantly. In this case, after designing our experiment we find ourselves waiting for some of the necessary materials to arrive. While this is a bit frustrating, this delay has provided us with an opportunity to meet with others in the lab and to get a better appreciation of what others have been doing. The lab that we are working in has a formal meeting once a week in which everyone is expected to share with the group the results of the various projects that they have been working on. During these meetings the fundamental importance of acting as a team in scientific investigation is very clear. Interesting data, mistakes made, bad jokes, and pastries makes for a fascinating experience although after 2 or 3 hours we are ready to get back into the lab. After each one of these lab meetings we feel that much more a part of a research team. Just like any team the sum total is much greater than the sum of the individuals themselves.

My fourth week:
The week began with our attendance at a conference that is also being held at BU and to which we were kindly invited. The conference is sponsored by the New England Board of Higher Education and is targeted at helping both secondary school teachers, as well as our university counterparts, in becoming more effective teachers. The need is particularly important in interesting students in potential careers in basic and applied science as the demand for such trained personnel is far greater than the number of appropriately trained students that we are generating.
Although a variety of techniques can be employed in developing more effective and engaging teaching, the conference was centered around problem-based learning approaches. One form of such an approach is the use of case studies. Some time ago, professional schools in business, medicine, and law began to incorporate the use of case studies in their curricula. Sometimes this approach is called problem based learning or PBL for short. Perhaps, you have already had teachers who have used such approaches in their own teaching. As part of the conference, we were given a real-life case study involving designing a more efficient and economical wind turbine. What really impressed me in doing this exercise, was the power in tackling the issue in small groups. The format helped catalyze our efforts, reminding me of how a good sports team is much more than the sum of its individual players. At the end of the exercise, it was interesting to compare the approach of our group with other groups, as well as with the actual proposal that the company involved felt to be most promising.
Much of our week was spent pursuing our actual research. We were busy growing and maintaining cultures of the bacteria that we are using for our experiments. After growing the bacteria, we then extracted the proteins from the cells by lysing them. This step basically involves using a fancy detergent to split the bacterial cells apart releasing the contents of the cells into the solutions. Following centrifugation (cells spun at high speed in order to separate the contents by density) the supernatant (the lightest fraction) will be used in our laser-based detection system. Unfortunately, we had to postpone our experiemental trial runs until the beginning of next week due to equipment availability. We can hardly wait to see the reults of all of our efforts!

My fifth week:
The week began with high expectations, however our results from our work conducted the previous week were disappointing. We had hoped for a successful outcome in which the proteins released by the bacteria that we had lysed would bind with their complementary antibodies. This did not happen. That's the great thing about science that in not getting the result we had anticipated we actually have a new opportunity in exploring other parts of the question. So we immediately began to brainstorm about what might be going on in our experiment. As a result we decided to add another strain of bacteria to be tested. This strain was similar to our original one, but we thought that the differences that do exist between the two might give us a better understanding of what was happening. We also modified the steps involved in processing the bacteria. Specifically,we added a series of freeze/thaw cycles that we hoped might better lyse the cells apart resulting in the release from the cells of those proteins that we hoped would bind with our antibody targets. Back to the lab! It was with high hopes that we grew up a batch of new bacteria and got them ready for another run. We prepared the chips that held the antibodies on Thursday and ran them with the bacterial lysates on Friday afternoon. We left for the weekend with high hopes that when we analyzed the results when we returned on Monday we would find that the changes that we had made in our experimental conditions would result in an outcome more favorable than our previous one. Can't wait to get back on Monday!

My sixth (and final) week:
Well, now we had the opportunity to view our results from our modified procedure. Surely, these would now work in the manner that they"should". Students often are surprised by the challenges and efforts that are often required in properly analyzing data and results. This was certainly true of the data analysis that we had to conduct. When we were done, we were faced with some interesting results. Once again, the antigens presumably contained in the bacterial cell lysate that we had generated failed to bind with the antibody on the chips, but this time we also found that some of the antibody itself appeared to have been lost during the trial! What could we then conclude with the end of our experimental work? In a sense we seemed to fail, that is we had not obtained the binding between bacterial lysate and antibody that we had hoped to achieve, yet this was hardly failure for we had achieved great success in learning about the system that we were using. We had answered some questions, and more importantly, we had generated a whole host of new ones. This is the art and beauty of the process of science itself. We left our lab fully confident that further investigation would ultimately demonstrate that bacteria in environmental samples could be accurately identified and counted with the IRIS system.
When we began this program almost 7 weeks ago with a set of introductory meetings conducted at Northeastern University prior to our start at BU, all of us were a bit anxious and unsure of where the whole thing would take us. At that point, I was having some regrets that I was trading a summer of having fun in the outdoors for a lab building in Boston. At the same time, our interest and excitement in new challenges, knowledge, and friendships, drove all of us on. Perhaps these feelings are very similar to how you first felt in entering BC High. Just compare those feeling with how you know feel! Well, it has been a wonderful experience and one that I hope to share with you in the classroom as we conduct our own investigations throughout the year!

Tuesday, July 6, 2010

Summer Sun, Fun and Photons?

Just like you, teachers look forward to the long, summer vacation. Like you, many of us escape to beaches, travel to new (or old) places, relax with friends or settle down with a good book. Sometimes, however, we return to the classroom (or lab) to renew, reinvgorate and explore. Unlike you, we do not have to attend, but elect to do this. I know, it sounds crazy and there are moments when I would tend to agree. Yet this summer when I was chosen, along with seven other teachers from throughout the state, to participate in a six week long research experience at Boston University, I was thrilled.
The name of the program that I am participating in is called "Research Experiences for Teachers" (or RET for short). The idea behind this nation-wide effort is that science teaching is enhanced when the teachers themselves have the opportunity to engage in actual research. I know that all of my students are thrilled when we leave our classroom behind and go to the lab to work and explore together. Although we may be a bit (or in my case, a lot) older than you, we still have that same feeling of excitement and anticipation as we set our textbooks aside and spark up the bunsen burner.
All of you are well acquainted with that first week of school feeling: what teachers will I have and are they easy or hard, where's the cafeteria, the restrooms, will it be fun, will I make friends? Well, despite my years teaching, as well as working in labs, I shared many of these same feelings. Although many years ago, I spent a semester at BU as an undergraduate, it is like a whole new school. The .....