Back To School

Now that the school year is under way, and the first few weeks have passed, things have calmed down enough that I am hoping to start working on continuing to develop my curriculum for my class integration of the concepts I learned while at ASU this summer working in the Center for Biological Physics. After familiarizing myself with my students and abilities, it is becoming clearer how I can integrate some of the concepts learned into the course in a beneficial matter. Many of the students in my math classes are also currently in Physics and took Biology last year. Due to this, they have a strong enough foundation in the background knowledge to grasp the concepts that I will be addressing in some depth. I am still struggling with how these concepts will tie directly into the geometry skills that the students are learning, however, I am seeing some possibilities for linking this material.

Day 19-crunch time

As a team, Rebecca, Stephanie and I have really begun to knock out our project. We were able to borrow some supplies from the Physics department and have begun to practice our lab that the students will be doing to go along with our project. It took a bit of time and work to get the kinks out of it, but we are ready to bring our newly gained knowledge back to the classroom and have a fun activity to relate real-world science applications to our math classrooms. We are still working to be ready for our presentation 1 week from today, but are excited to show off all that we have learned.

Day 18- poster and project time

I came into the center for Biological Physics today with a more positive attitude and an excitement to continue on developing our curriculum for our classroom while continuing to progress on our poster. We had a lecture this morning by Daniel Barr on molecular dynamics, time steps, and simulations. It was difficult to focus on the lecture because we each wanted to dive into our curriculum now that we have such great ideas to push forth in our classrooms. Now that we have gotten our idea that is the purpose of the program, it is difficult not to focus on this every second!

Day 17- The Biodesign center

Today we had the privilege of touring the biodesign center with Dr. Stuart Lindsay. On this tour, we were able to witness the many open labs which are specially designed to facilitate communication between the different research groups and encourage collaboration rather than just working individually with one's research group. This allows for greater opportunity to advance because there are more people to tap into and those with specialties in one area can help to bridge gaps in understanding for researchers in another field or another area of the field.

After the tour, we broke into our small groups and bounced ideas around for our curriculum project and began developing our project. We had our official "aha" moment today and began to compile our curriculum ideas because we have a hook to bring in our students and tie our math into their world and the world of science at the same time. We are operating on the principle that math is the language of science, so without math, you cannot understand and use science fully. With this statement we are ready to bring science and a relevancy of math back into our high school math classrooms!

Day 16-Forming our groups

Today, we officially divided into our poster/project groups. Dr. Ozkan helped us to finalize our teams as well as our researcher whom would help us with the details of our project. We have decided to work with Daniel Barr, a graduate student of Arjan van der Vaart. He has been a big help to us thus far in taking the research done in the center and translating it into a form of information which we could understand. I am excited but also a little nervous because our posters are due a week from today and we are still struggling to come up with a hook to bring in our students and show them the ties between math and research science. In addition, what I am really hoping to take out of this project is the knowledge of all that is left to discover in the field of science. So many students are discouraged by the field of science because they do not realize how much is left to be discovered. This program has shown me how much is available for our students to contribute to the world of science.

Day 15- Starting week 4

Today I started in the CBP with a bit more stress than usual. I have realized how close to an end we are with our time at ASU, but I am still struggling with the concepts of my research and how to apply this in the classroom. Today's lecture was given by Dr. Arjan van der Vaart. He gave us a deeper understanding of molecular dynamics and the reason for doing this rather than lab research. Some of the benefits include cost, rarity of certain materials, prevention of exposure to dangerous chemicals, and more detail into changes that happen over such a short period of time that they would not be readily observed in an experiment. We have started to form groups and will decide on researchers tomorrow, which gives me hope for completing our project in a way that it will truly help my students to understand the practical applications of geometry and algebra in the fields of science, primarily physics and biology.

Day 14- end of week 2

Today we worked with Dr. Michael Thorpe again on structural rigidity and formation of proteins. The popsicle stick model has led to a well developed formula for determining the degrees of freedom of any structure based on the number of atoms and the number of bonds. This is a great algebraic and geometric concept that I hope to implement in my classroom this school year. I am still struggling to come up with my own, unique model of tying this into my classroom, but hopefully, as we join our own researcher next week, we will be able to bounce ideas off of one another in smaller groups and be ready to go!

Day 13

Today was another valuable day with Dimitry. We discussed more modeling software, which is great for visualizing the actual workings of the proteins. The only difficulty I am having with this is that we have been exposed to so many protein modeling software programs, but have just had a brief overview with each of these. I am hoping that next week, when we divide up with our actual researcher, we will work with just one visualization program and be comfortable with this rather than just having an overview of many programs with no actual deep understanding of how to best use each program.

Day 12- Dr.Thorpe, popsicle sticks, and Polytechnic campus

Today was my "light bulb" day in the Center for Biological Physics. We met Dr. Michael Thorpe for the first time today. This was also the day that we were truly able to benefit from our mentor teachers from last year. This group had created an activity about rigid and non-rigid structures of proteins using Popsicle sticks of different lengths. Then, the mathematical counting principle of determining the degrees of freedom came into play. This was an exciting day for me because it is all finally starting to come together. I now am seeing ideas that could play well in my Geometry classroom.

After this, our afternoon was spent at the Polytechnic campus. My favorite part of the day while visiting the Polytechnic campus was the LARB, or the Lab for Algae Research and Biotechnology. In this lab, they are growing different types of algae to determine beneficial uses for this such as an alternative energy source. This was exciting because it is actual research happening that is a hand's on experience.

Day 11- Dr. Ozkan

Today's lecture got into the specific details of why protein folding is such an important field of study. Protein folding is an important concept because if we can figure out how and why proteins fold the way that they do, then we can figure out why they misfold and what can be done to correct misfoldings of proteins. After this is done, we can better develop drugs to overcome this protein misfolding that results in diseases such as alzheimer's disease. After this, in order to help with compiling ideas for our projects, we discussed some mathematical applications such as calculating the angles between atoms on the protein chains. This is a bit higher of a mathematical concept than my course addresses, but it did get the ideas flowing for some possible projects involving angles, polyhedrons, and 3-dimensional shapes that mimic formation of proteins. I have some ideas regarding transformations of atoms to form amino acid chains, and the resulting proteins as an applicable geometry project.

Day 10- 2 weeks in

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.

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.

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.

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.

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.

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.

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.

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.

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.