TEqb

Tuesday, August 8, 2006

So, this is the last blog of the summer.  I can't believe this is the last week.  It's gone by so fast.  It feels like just yesterday we all met together in the Gilbreath hall.  When I was coming into this program, I had no idea what to expect and who I would meet.  But it worked out well because we learned a lot and seemed to have made great friends.  I'm going to miss seeing people everyday.  Also, I've gotten to know the REU guys, and they are so much fun to hang out with.  It took a while to actually start hanging out with them but after the camping trip, I feel like we all know the REU people better and the same on their part.  I think the saddest part of this program being over is that I don't get to see Patty or the REU guys anymore.  Hopefully though, some day our paths will cross again.

Lately, we've been having lectures about fractals, monte carlo methods, and complexity in the mornings and working on our projects during the afternoons.  I'm doing the fractal biology project, which is interesting but hard.  Katie, Alex, Nicole, and I are working on the project together.  We still haven't figured out how to make a fern in just basic quite yet but hopefully we'll figure it out by tonight or tomorrow.  Dr. Yampolsky has been helping us on it.  So, we are trying to make our presentation actually interesting and fun rather than boring.  We were thinking of putting in pictures of fractals and having a hands-on activity to get everyone involved and listening. 

Dr. Knisley taught us on Monday about fractals and chaos.  He started out by talking about self-similarity and different dimension.  Barnesly said "Any image can be approximated by a fractal." in his Collage Theorem in the 1980s.  I found that quotation very interesting. 

I hope everyone else had as much fun as I did.

TEqb

Thursday, August 3

TEqb

Tuesday, August 1

We've been doing a couple things lately.  After learning about prokaryotes and eukaryotes, we learned about phylogenies.  We learned phylogenies with a game where we had schmooms, which are aliens from a different planet, and tried to figure out which was the outgroup and ingroup and what the ancestors where.  We demonstrated our understanding of this game by doing homework and figuring out how many topologies you'd get from 3, 4, and 5 species.  There is a formula that shows the increase in species.  It's (2n-3)! / (2^(n-2) * (n-2)!).  Other homework was to draw a phylogeny and find the ancestral states of four certain species, which was a good way to make us think and connect how each one relates and see which species are closer than others. 

On Friday, July 28, we went to Oak Ridge National Laboratory.  It was really exciting.  I actually followed the bus down in my own car, so I could go home straight after.  So, I missed out on the bonding on the bus.  When we got there, we went to see the first continuous reactor.  It isn't used anymore but was the start of making plutonium.  We also went to the mouse house.  Sadly, we didn't get to see any of the mice but we learned about phylogeny correlating with mice and how mice are the closest related mammals to humans.  We also got to learn about the five projects that the laboratory is working on at the moment.  One of them consisted of proteins, which is a field that interests me.  They suggested getting an internship there.  So, I was thinking of actually taking that opportunity.  We also got to go see the big computers.  That was neat.  The last place we went was to a place where they simulate live streams and see how different environments such as strobe lights affect the fish.  I thought that field trip was the most educational and helpful one so far for research.

TEqb

Thursday, July 27

On Monday, July 24, we began the day with Dr. Knisley teaching us about the Life Cycle Diagram.  The life cycle diagram and the equations that Dr. Knisley explained to us were related to the predator-prey problem.  I really liked the different types of computer programs Dr. Knisley wrote to illustrate the spread of a rumor and epidemics.  It helps show the problem visually then just trying to visualize it.  You can find his programs at http://faculty.etsu.edu/knisleyj/biomath/ to get a feel of what weve been learning.  So, in the life cycle diagrams, Dr. Knisley used an S for suceptibles, I for infected, and R for removed.  The life cycle diagram looked something like this: S -> I -> R.  The logistic equations that explain this diagram were: S' = -alpha*I*S, I'=alpha *I*S - b*I, R'= b*I.  Also, that day we learned about the five choices we have for our hands-on project.  Three of them looked appealing to me but I picked doing fractal biology.  We have to find a way to create fractals on the computer and learn about how fractals and biology correlate.  The little research that I have done on this topic has brought up fractals and chaos. 

            On Tuesday, July 25, we learned about code and messages and how the genetic code works.  I enjoyed learning about the properties of genomes from the first principles.  The properties are the genome must be long, aperiodic, error resistant, and self-replicating.  We also learned about gene expression, but this was review for me because I learned it in AP biology.  We had Dr. Miller teach us for the first time on Tuesday.  He explained Polymerase Reactions.  I understood what Dr. Miller said because we did a lab just like it last year in biology.  So, that was helpful.  To finish up that day, we learned how to use probability and find the frequency of genetic codes appearing in a certain sequence. 

 

Tuesday, July 25

This past weekend we went to the Natural Tunnel State Park to do some field biology such as ecology and botany.  We also went on some hikes to see the tunnel.  We ended up going with the Math research group.  They are here for the summer to do a math research program with Dr. Godbole, and we usually play soccer and ultimate Frisbee with them.  So, five of the guys from that program came up and camped with us, which made it more fun because there were more people.  Anyways, the first day we got there and went swimming before we went on our hike.  The first place we hiked was to the tunnel.  On our way, we learned a lot about different types of trees such as dogwoods and tulip poplars.  We also learned about mushrooms, ferns, and other plants.  On the way back from the Lovers Leap trail, Dr. Yampolsky told us that the trail was originally made by sheep, who know the best way to go down mountains and conserve energy.  I thought that was an interesting fact.  The next day was really fun because we learned about flowers and plants and how to classify them.  We learned about the pea, aster, mint, and carrot families.  We learned how to identify each family from their petals, fruits, and fluorescent.   After that, we went down to the tunnel and went inside.  I really enjoyed crossing the water and seeing the way the tunnel was created.  When we were in the tunnel, the train came by and being next to it was kind of frightening but pretty exciting also.  The last day was probably the most fun because we went into this lake and looked for fish and mussels.  This trip was the best one we've had so far, and we all got to know each other so much better. 

TEqb

Thursday, July 19

It has been about a week and a half.  It has been interesting.  I really like all the people in the program.  We seem to all be really different but click really well.  We work really well together on our homework.  Lately we've taken independent probabilities and elaborated more on them through conditional probabilities.  We did one problem about a patient having the chance of having a disease or not having it and false negative and positives.  To figure out the percentage of this, we learned Bayes theorem.  Then, the day after we learned from Dr. Godbole how to use Bayes theorem with genetics such as what is the probability of a child being Aa if the father is AA or Aa while the mom is aa.  The chance is 2/3.  Also, we learned the probability of getting a 7 when you are playing crabs.  We've also learned about capture-recapture which is an interesting topic.  This helps us find the estimation of animal abundance in a specific area.  There is also another way of finding the animal abundance.  It's line transect where you go over a certain area and count how many specific animals there are and then set up a ratio to find the animal population in the total area.  This week weve also had a new teacher, Dr. Knisley.  He teaches math and has published a lot of research.  He showed us some of his work today.  He does a lot on neuroscience.  Lately though, hes been teaching us about intrinsic rate and how its equal to slope over actual.  Today he taught us that slope over actual is equal to the first derivative over y.  I really like calculus so having it come up and being able to use it in research will be something I look forward to.  Our latest homework is about population models and epidemics.  The question is what factors are important in an epidemic model?

TEqb

Monday, July 17