The Bugs Have Bitten
Week #3
You know that little homesick bug I recently mentioned? Between eight hour days at the office, my new found insistence and craving to lap swim almost every day, and taking late night runs to In N' Out with my roommates and friends, I can hardly even feel the bites filled with the longing to be back in my normal life. Occasionally, however, they itch a little bit - forcing me to remember the familiar, caring faces of family and friends and the chillaxing days in town, sitting on the benches and playing sand volleyball in Town Park. The visit of my grandma and her almost-sister this weekend has helped heal the annoying bumps; getting away from campus and into the city has been quite medicinal and not to mention the amazing "Coast Toast" featured at a cute little house-looking restaurant called Brockton Villa right on the beach in La Jolla. But, nevertheless, the persistent reminder that I'm at least 1000 miles from my bed and not going to see my mom for another 4 + weeks makes my heart a little sad.
Don't assume I'm actually ready to go home to the chains of 2-a-day volleyball practice and set in stone rules just yet though - there's still so much to be seen and done here! This weekend, I got to see a bit of San Diego with my Texan "grandmothers" who happen to love the waves and flowers of California. Between eating at the Hard Rock cafe downtown in the Gaslamp District and getting a "scenic" tour of the city by taking some wrong turns and misreading a few maps, we've gotten to see many historical landmarks and famous places. Tomorrow, we're off to Coronado Island to have brunch at the stunning Hotel del Coronado and possibly visit the famed San Diego Zoo or the USS Midway. In any case, having the opportunity to get off UCSD property and out on the town is yet another perk of this internship.
Mild homesickness is not the only bug I've encountered this week - there was also a computationally small but large impact glitch found in the JDOCK program I'm using at the "lab." Simply put, JDOCK is supposed to use two ligands to create "children" while groups of atoms are added to others to create "mutants." Everyone knows that to create a child, you need 2 parents and that’s exactly what the program didn't have. More specifically, the program was creating .dlg files with no .pdb files to back them up. Basically, we had the information regarding a specific ligand but no picture to display it. Anyways, the chance that this error was actually caught is somewhat rare so it's in some ways good that it occurred during the earliest trials. Unfortunately, it does affect all of the data we've collected on the N1 neuraminidase but running all of the JDOCK "jobs" would take too long and may prove completely unnecessary.
Personally, I think one of the best and most interesting features of this program is the fact that, even if you use the exact same files, parameters, and specifications, you will always get different results. Since the mutant ligands are made using a random fragment library, there's no saying how good or bad they will turn out. The unpredictability of it is fascinating - especially in a scientific world that is so precise and exact. This experience is very similar - compared to the routine everyone is used to and comfortable with at home, much here is spur of the moment, occasionally filled with bugs, but overall unexpected and gratifying.
You know that little homesick bug I recently mentioned? Between eight hour days at the office, my new found insistence and craving to lap swim almost every day, and taking late night runs to In N' Out with my roommates and friends, I can hardly even feel the bites filled with the longing to be back in my normal life. Occasionally, however, they itch a little bit - forcing me to remember the familiar, caring faces of family and friends and the chillaxing days in town, sitting on the benches and playing sand volleyball in Town Park. The visit of my grandma and her almost-sister this weekend has helped heal the annoying bumps; getting away from campus and into the city has been quite medicinal and not to mention the amazing "Coast Toast" featured at a cute little house-looking restaurant called Brockton Villa right on the beach in La Jolla. But, nevertheless, the persistent reminder that I'm at least 1000 miles from my bed and not going to see my mom for another 4 + weeks makes my heart a little sad.
Don't assume I'm actually ready to go home to the chains of 2-a-day volleyball practice and set in stone rules just yet though - there's still so much to be seen and done here! This weekend, I got to see a bit of San Diego with my Texan "grandmothers" who happen to love the waves and flowers of California. Between eating at the Hard Rock cafe downtown in the Gaslamp District and getting a "scenic" tour of the city by taking some wrong turns and misreading a few maps, we've gotten to see many historical landmarks and famous places. Tomorrow, we're off to Coronado Island to have brunch at the stunning Hotel del Coronado and possibly visit the famed San Diego Zoo or the USS Midway. In any case, having the opportunity to get off UCSD property and out on the town is yet another perk of this internship.
Mild homesickness is not the only bug I've encountered this week - there was also a computationally small but large impact glitch found in the JDOCK program I'm using at the "lab." Simply put, JDOCK is supposed to use two ligands to create "children" while groups of atoms are added to others to create "mutants." Everyone knows that to create a child, you need 2 parents and that’s exactly what the program didn't have. More specifically, the program was creating .dlg files with no .pdb files to back them up. Basically, we had the information regarding a specific ligand but no picture to display it. Anyways, the chance that this error was actually caught is somewhat rare so it's in some ways good that it occurred during the earliest trials. Unfortunately, it does affect all of the data we've collected on the N1 neuraminidase but running all of the JDOCK "jobs" would take too long and may prove completely unnecessary.
Personally, I think one of the best and most interesting features of this program is the fact that, even if you use the exact same files, parameters, and specifications, you will always get different results. Since the mutant ligands are made using a random fragment library, there's no saying how good or bad they will turn out. The unpredictability of it is fascinating - especially in a scientific world that is so precise and exact. This experience is very similar - compared to the routine everyone is used to and comfortable with at home, much here is spur of the moment, occasionally filled with bugs, but overall unexpected and gratifying.
Add a Comment
-
Comment by Barbara M. Waitz on July 13, 2008 at 1:32pm -
Hi Meghan, wanted to let you know I am fascinated by your descriptions of expeirences as an intern. Love hearing from you about your activities at the U. and with Mimi and Frances--glad they came to enrich your visit to San Diego.
Will be seeing your Mom this week in Boulder when she comes for Mandie and Aaron's wedding. Know that missing family and friends can "bite" a bit, but having the opportunities for growth you are gaining is also worth the pangs of being apart.
Yep, science, too, can be unpredictable. In fact, that's the WHY of doing science--to discover how to make the unpredictable predictable! (Many of us enjoy the bizarreness in the world, but we depend upon the near-certainties--like gravity (?) And now, even gravity is being questioned!)
I loved your writing that "Everyone knows . . ."--which is exactly the kind of "assumption" that scientists like to question! Boy, are you going to be sharp when you return to Telluride. I pity your science teacher! (Just kidding, of course!).
Everything is fine here, including me. John and Galen were here for 3 weeks while Galen went to a camp in Boulder. John did all kinds of jobs around my place, and it's looking better and better now. i also enjoyed their company since I spend a lot of time alone--not lonely, though.
Plan to drive over to the Western Slope early in the fall. I am looking forward to seeing you with your new haircut. (John showed me how to rotate your pictures so I can see you without lying down.) Meghan, you are just plain beautiful! Both John and I had some trouble recognizing you--you look so grown up! You've lost your "chubby baby" cheeks! I'm surprised that the freshmEn (and others) at the U. of C. haven't been lining up to date you, but your Mother says there aren't any in your lab. Shucks!
Love visiting with you, and want you to know how happy and proud I am to be your grandma.
Treasure your open-minded approach and enjoyment of learning--a lot of people lose that before they are 17!
Loads of love, Mama
About
© 2009 Created by WonderDog on Ning. Create a Ning Network!
You need to be a member of Pinhead Institute 2008 Interns to add comments!
Join this Ning Network