Today was begun with another lecture by Daniel Barr. Today's topic was on his specific research on the protein Lactose inhibitor. This is a protein that interacts directly with the DNA and prevents specific parts of the DNA from being active. This is of interest because if we can determine how certain areas of the DNA are supressed we can then work to stop DNA mutations by preventing the DNA from expressing these dangerous genes.
After our morning lecture, we had time this afternoon to work on separating into our groups and beginning to compile ideas for applying our knowledge gained in the lab into our classrooms. Wendy, David, and I have started compiling ideas involving experimentation and probability or possibly structural rigidity of protens. We still have three weeks, but it feels good to have a group established and beginning to get ideas flowing.
Friday, June 27, 2008
Thursday, June 26, 2008
Day 9- Meet Dr. Stuart Lindsay
DNA sequencing is an area of science that I have always possessed a strong interest in. Today, Dr. Lindsay explained the randomness of DNA formation and sequencing. The other main focus of the lecture was on the benefits of Polymerase. Another area of interest in today's lecture was on exons and introns in DNA sequencing. Exons are the expressed genes in DNA strands whereas introns are what used to be considered "junk DNA" because they were not expressed genes and therefore scientists did not view these as important. Today, however, it has been revealed that introns, while not expressed genes, are necessary for several controlled functions within each cell. From today's lecture, I hope to bring back to my students the vast need for more research into the sciences. The human genome project has left much more work and unanswered questions that will need worked on by our students in their future.
Day 8- Dan Thorpe
Today at the Center for Biological Physics, we met our third doctoral student, Dan Thorpe. Dan took time to educate us on the physics related to protein folding and creation of proteins. This involved a great deal of calculus in the form of partial derivatives of formulas. The most beneficial part of today's lecture was gaining examples to show higher math students the practical applications of their calculus skills in a thriving field of scientific study.
In the afternoon, I was able to gain some invaluable skills in excel text manipulation. In my databases, I like to sort by last name, but then I use the information in letters where I would need the first name to occur first. I learned a method of separating the first and last name and putting them in the correct order to make my workload much lighter in this aspect.
In the afternoon, I was able to gain some invaluable skills in excel text manipulation. In my databases, I like to sort by last name, but then I use the information in letters where I would need the first name to occur first. I learned a method of separating the first and last name and putting them in the correct order to make my workload much lighter in this aspect.
Tuesday, June 24, 2008
Day 7- More databases
Today we worked with Kirill. He was able to instruct us on more programs that can be used to view protein structures online. In addition to this, we were able to view some programs created by Dr. Thorpe and others through flexweb at http://flexweb.asu.edu/. This website allowed me to obtain a more visual understanding of protein bonds and flexible and rigid protein structures. My favorite program of the day was the 2D pebble game which allowed one to determine if structures were rigid or flexible.
Monday, June 23, 2008
Day 6
In the Center for BioPhysics today, we met our second doctoral student, Daniel Barr. He is a doctoral student of Arjan van der Vaart. Because Arjan is currently out of the country, Daniel stepped in to give us some insight into their field of computational biophysics. Today, we were given a great deal more information on structures of proteins. The most interesting aspect of today's program was learning about the proteiome project. This is another level to the human genome project. When studying the human genome, it was realized that more information would be needed regarding the specific proteins that are created by the genes in order to more fully understand complex organisms, hence the focus on the study of proteins. We also viewed more freeware programs which allow you to view the structure of various proteins in great depth. This also allowed for a 3-dimensional view of proteins.
Friday, June 20, 2008
Day 5- onto the computer simulations
In the Center for BioPhysics, the majority of work is based on computer simulations. Today, with Dimitri, we downloaded our first programs that would allow us to view many protein structures. This program was very interesting because it provides an excellent visual of actual proteins and their resulting structures. Another tool that was used in conjunction with this is the protein data bank. This is located at the website http://rcsb.org/pdb. In order to view the many proteins presented on this site, the Rasmol viewer or another protein viewer is needed. The freeware protein viewer is located at http://openrasmol.org.
In order to best understand these views of the proteins, it is important to understand some basics about proteins. All proteins are comprised of the 20 different amino acids. Of these 20 amino acids, 2 have a negative charge, 2 have a positive charge, 3 are polar, and 13 are nonpolar. These different properties of amino acids are what result in the various protein structures of strands or helices.
This afternoon, we will be attending a series of small mini-workshops on a variety of subjects to see if there are specific topics that would be beneficial to gain more insight on in order to build on our teacher's toolkit. I am looking forward to further training on Geometers sketchpad.
In order to best understand these views of the proteins, it is important to understand some basics about proteins. All proteins are comprised of the 20 different amino acids. Of these 20 amino acids, 2 have a negative charge, 2 have a positive charge, 3 are polar, and 13 are nonpolar. These different properties of amino acids are what result in the various protein structures of strands or helices.
This afternoon, we will be attending a series of small mini-workshops on a variety of subjects to see if there are specific topics that would be beneficial to gain more insight on in order to build on our teacher's toolkit. I am looking forward to further training on Geometers sketchpad.
Day 4- Meet the doctoral students
Today started off very differently from the past 3 days at the Center for BioPhysics. Rather than receiving a lecture delivered by one of our professors, today's lecture was delivered by one of the doctoral students in the department, Adam de Graff. Adam's lecture was on DNA, inheritance, and the struggle for survival. In short, this lecture discussed the building blocks of DNA, the primary theories involving the creating and development of DNA, and the evolution of DNA from the earliest organisms to modern, complex organisms of today. Another important aspect of the lecture was on the causes of evolution. The two primary causes of evolution that were discussed were DNA mutations and recombination of DNA. This lecture was extremely beneficial to me for two reasons. First, this was the first day that I truly felt that I had a grasp on the concepts of the lecture and could explain the received information with a level of clarity. Next, this information was delivered by Adam with such intensity and enthusiasm for the subject that it kept you engaged throughout the lecture.
In the afternoon, we were once again split into our groups. Once in our groups we discussed two questions relevant to the math and science teachers in this program: funding for hands-on activities in the classroom and practical applications of science and real world phenomenon in the math class. There were many beneficial concepts and ideas presented by my peers that I feel will help me in my planning for the upcoming fall semester.
In the afternoon, we were once again split into our groups. Once in our groups we discussed two questions relevant to the math and science teachers in this program: funding for hands-on activities in the classroom and practical applications of science and real world phenomenon in the math class. There were many beneficial concepts and ideas presented by my peers that I feel will help me in my planning for the upcoming fall semester.
Thursday, June 19, 2008
Day 3- MSTF
Today started out with another in-depth lecture by Dimitry regarding protein reaction centers, and the efficiency of photons in creating energy as opposed to other methods such as silicon or molecular-created energy. This concept was also highly above my ability level in many respects, but there were many biological concepts that I was able to grasp that helped to give me some understanding of the overall topic of the lecture. While much of this information is very fascinating, I still have not found any ideas as to how to apply this to my content area at the high school.
In the afternoon MSTF class, we first had our required safety-lab training. While this was not full of excitement, it was needed to be safe in the lab. However, in my area, we are not in a lab, so it did not have a lot of application. After this, we learned of some mini-workshops that will be presented by our peers within the program to build or skills in areas such as PowerPoint, Google Documents, and Geometers SketchPad. I am looking forward to this in order to build some of my skills for the upcoming school year.
In the afternoon MSTF class, we first had our required safety-lab training. While this was not full of excitement, it was needed to be safe in the lab. However, in my area, we are not in a lab, so it did not have a lot of application. After this, we learned of some mini-workshops that will be presented by our peers within the program to build or skills in areas such as PowerPoint, Google Documents, and Geometers SketchPad. I am looking forward to this in order to build some of my skills for the upcoming school year.
Day 2- the CBP professors
Today, the Center for Biophysics groups had a chance to meet with 2 of the professors that will be our insight to the research in their field as well as our teacher mentors, the 3 teachers that were in the program in this area last year. It was very beneficial to hear from Brian, Fred, and Rich and realize that these 3 were in the same place of high frustration regarding the intensity level of the program and the lack of actual lab work. However, after seeing their developed project from last year, I see a light at the end of the tunnel in regards to potential for curricular activities within the field. I see many ties right now to higher levels of math such as calculus and trigonometry, but because I am teaching lower levels of math, I will work to find more relevant applications to my field.
Today, Professor Dimitry Matyushov lectured on Molecular Dynamic Simulation. After leaving lecture, I felt 1, as if my head were about to implode, 2 like laying down for a good cry, and 3, like he had talked in a foreign language the entire time. Though I was able to interpret a few of the formulas, the concepts were too high of a level for me to grasp. Today's lecture did, however, serve to show the vast potential for continued research in the sciences and how much we truly do not know yet. This is a new view of science for many of my students that I am hoping to show them because many consider that the field of science is very well discovered and there is not a great potential for continued discovery, while in all reality, it is just the opposite.
Our other lead professor, Dr. Banu Ozkan, has given us some backgroup information into her field, which specifically involves a theoretical approach to protein folding. Once we are able to understand how and why proteins fold, it will provide insight to Alzhiemer's and Parkinson's disease, which are both as a result of protein misfolding.
Today, Professor Dimitry Matyushov lectured on Molecular Dynamic Simulation. After leaving lecture, I felt 1, as if my head were about to implode, 2 like laying down for a good cry, and 3, like he had talked in a foreign language the entire time. Though I was able to interpret a few of the formulas, the concepts were too high of a level for me to grasp. Today's lecture did, however, serve to show the vast potential for continued research in the sciences and how much we truly do not know yet. This is a new view of science for many of my students that I am hoping to show them because many consider that the field of science is very well discovered and there is not a great potential for continued discovery, while in all reality, it is just the opposite.
Our other lead professor, Dr. Banu Ozkan, has given us some backgroup information into her field, which specifically involves a theoretical approach to protein folding. Once we are able to understand how and why proteins fold, it will provide insight to Alzhiemer's and Parkinson's disease, which are both as a result of protein misfolding.
This is some of the notes from our day 2 lecture on entropy and ideal gas law.
Day 1- MSTF
Day 1 at the Math and Science Teacher Fellows program led to a variety of invoked emotions. I came into this program excited at the potential of integrating science into my math program. As a math teacher with a science background, I see how closely related and interdependent these fields truly are, and therefore, I came into this with great enthusiasm toward achieving this goal. Learning in slightly more depth about the variety of fields that my peers would be involved in served to further peak my interest in this program. When learning about my field, I was a bit stressed about the high level of physics involved in my research area with the Center for Biophysics. However, I am viewing this as a learning experience and a chance to greatly broaden my horizons. I am hoping to gain many new ideas that I can incorporate into practical applications of math in science in the classroom.
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