Student Research at Duke

Well I am out of the academia for a month now. It was a good time, you should definitely apply (even if you haven’t decided you want to come!) The application is free and only requires 1 recommendation (!!!) so as Hilary says, WHY NOT?!?! Anyhow. I learned a lot of stuff about a wide range of subjects, from molecular biology to math. The guest lecturers were pretty interesting, except for three (the lemur lady, the plant lady, and the AIDS/”sex workers” lady). I’m sure their topics were well interesting to people in their field, and maybe some of you guys will find it interesting and decide to do some bogus science (the plant lady wasn’t talking about her research though). The ethics were also bogus, I don’t believe in ethics.

That was my experience, but it’s pretty individualized so you get to do whatever you want to. Anyhow, to ALL MY LOYAL READERS out there, unfortunately you may not hear any more words from the Prophet, but I’m sure you’ll manage. Now I got four more weeks to kick back away from DA BOOKS.

The research program is almost over, and while I shall no longer be a Fellow (note the caps please) it shall still be entertaining. I can’t wait to return back to Chicago, but I still have a lot to do. My research isn’t really finished yet, I still got a lot of thinking to do (come to the POSTER PRESENTATION if you wanna find out what). I also gotta start getting a move on those MCATs, ewwww. Who names their exam the MCAT. But it’s been a draining if not stressful 8 weeks, I will probably reserve some FUN time for myself, or possibly find OUR HEROINE! (847 322 9534!! Don’t call unless you’re FINE with a capital F).

Many happenings in the world to speak of in the past 8 weeks! Since I would be the greatest policy-maker ever, let’s run down by them!! MICHAEL VICK … dubious… I SAY NOT GUILTY! That’s right, our hero doesn’t feel the urge to JUMP ON THE BANDWAGON, like some OTHER people. (and not just because he’s my #2 QB on my fantasy team ). Dogfighting? gmafb. INNOCENT UNTIL PROVEN GUILTY?!?! He speaks the truth! VICK4LIFE!

David Beckham to LA!! Soccer is a fun sport, people should watch. Maybe David will bring them, plus he’s still a solid center mid! BECKHAM CROSS TO DONOVAN!??!!? YOUR HEARD IT HERE FIRST! (probably not, but that’s okay).

Nocioni resigned for humploads of money. EXTREMELY DUBIOUS He’s good and all, but EIGHT MILLION DOLLARS GOOD?! I wouldn’t spend 8 mil for anything except 1) getting closer to KB24! 2) BEN GORDON!!!! 3) adding 30 seconds to my glorious life. Hopefully we get to trade him for THE MAMBA. The dream IS ALIVE!

JoJo wants to trade Nocioni

Of course sports are not the most important thing. Primaries are soon, and while I would not like to reveal my political affiliation (they warned us against doing that!), I endorse RON PAUL. RON4PREZ, he will catapult America into FREEDOM. Ron has a plan to solve immigration AND unemployment at the same time! Abolish the minimum wage! That way, no incentives to hire illegals and more jobs available! Ron has a plan to solve the energy crisis and terrorism - STOP SUPPORTING THE ZIONIST REGIME! Ron has many more plans, but I don’t wanna amaze you too much for one day. I HAD A DREAM!

Anyway, some words of advice from a the greatest. you should definitely apply for the Program, it’s easy! It’s well suited to your interests too. I had a good time, greatest roommate ever?!, greatest mentor ever!! Indeed. These last few days I just plan to pack stuff and study a little bit. Can’t wait to go back, but I had a great time (and will continue my research in the school year most likely!!) Perhaps I shall even post one more time for all my loyal readers (sorry about deleting all my fans’ messages, but they looked too much like spam unfortunately don’t worry I read all your RAVE REVIEWS!)

You haven’t heard about my research for a while, but I will add it… soon. Today I will blog about careers. Last week we had a “Career Panel,” where some graduate students talked about their adventures in academia. That was well interesting and all, but it didn’t really change what I think about my career. To tell you the truth, I always really wanted to be a lawyer, like Eugene on the practice. He was da bomb, as the kids say. The DA Lara Flynn Boyle would come in with her “solid case” and she’d be like “here’s my deal, take it or your guy gets life.” Eugene would just glare at her and say “LEMME THINK ABOUT THAT…. no, fu, see you in court.” Then Lara Flynn Boyle would say all these complicated things and the jury would be like “hmm.” But when Eugene crossexamined, he’d just ask “how do we know YOU didn’t kill so-and-so!?!! I GOT YOUR REASONABLE DOUBT RIGHT HERE!!!!” Then the guy would mess up and he’d point out something clever. Then Lara Flynn Boyle would give some BS closing, to which Eugene would reply “I won, why do you even try.” Then the judge would ask, “Jury, what say you?!!?” Then the jury guy would say, “We find the defendent, so-and-so,… *DRAMATIC PAUSE*… NOT GUILTY!” Bobby and his murderer wife would have their funtime, the huge mean lady would contemplate their ethicalness, but Eugene would just glare at people and say “u suck good game no rematch” (obviously because of double jeopardy). UNFORTUNATELY, I doubt I have the lawyering abilities. Watching Shark and Boston Legal is still entertaining though.

ANYWAY, while I don’t know exactly what I want to do, but I have a vague vision. I see myself surrounded by tons of money and a hot trophy wife. On the weekends, I shall play golf with Puff Daddy. Therefore, my vision severely restricts my career options. I shall be a physician or scientist, perhaps, or an MD/PhD. While research is entertaining and worthwhile, I haven’t really seen what it’s like to be a doctor, except for House and the Discovery Channel (and that’s mostly plastic surgeries). And it seems pretty damn awesome. I don’t know what I’d like to do exactly, but cutting people up, messing around with their guts, and stitching them back together seems fun. Anyway, while most scientists probably won’t make the kind of money I need to hang with Mr. Combs, I could be the exception. Winning the Nobel gets you a little bit of fame, that could be an option!! Alas, although I am wildly optimistic, I don’t know if I will ever win! (after all, these things are partially LUCK-BASED! Dubious). Maybe I could be like Marshall on Alias, or Q. After a while of brilliant innovations for some spies, I would build a giant weapon and have some fun with it. Or perhaps like those scientists in the scifi dystopia movies, where I make some extremely useful technology that no one live without and then I rule everything, until some young kids ruin my plan and they push me off my company’s thousand-story building while the world is liberated. That’s all for the future though, for now I just gotta keep working, studying, and having a couple laughs. Stay in school, kids.

Puff Daddy knows what a career’s all about.

The project continues to go well. Our hero just got back from the lab and wrote up a draft of the diffusion simulation! If Jason tries really hard then perhaps he can get a movie up by next week! He shall explain the research a little more now, get ready!

Okay so in the brain there’s neurons. And they basically control all your mental functions by working together and transmitting signals etc. It seems kinda odd how such a simple structure could result in stuff like memory, learning, etc. Well, one of the fundamental mechanisms of memory and learning is changing the strength of the synaptic connections (this is called plasticity). Anyway, the way plasticity works (or at least part of it) is changing the amount of receptors of the neurotransmitter on the postsynaptic side. We’re looking at the glutamatergic synapse, and the receptors are called “AMPA receptors.” So people have found out that they diffuse laterally in the membrane (it’s just a lipid bilayer, so that makes sense). Anyway, the diffusion is kinda complicated and theres a bunch of other stuff that affects it, so we’re trying to model the dendrite system. The basic question - what are the consequences of diffusion? So that’s a brief summary.

Anyway, I just started on the actual diffusion simulation right now. The program is halfway over, so I’m hoping that I can finish it and get some results soon. I might come back and work in Dr. R’s lab after the program also, WE SHALL SEE!

In other news, the Bulls select JOAKIM NOAH with the 9th pick. ‘Twas a sad day for Chicago, because Milwaukee STEALS Yi! THE DREAM IS DEAD! #^#$%^!@. I have no words for such a travesty, since this is a research blog and we were told to keep it pg-13.

Joakim: “I’m gonna crush Milwaukee for taking Yi!”

Oh well, Joakim is a nice addition and HOPEFULLY he will magically develop a low-post game in a couple months! In two years, a 20/20 player? Perhaps! (but dubious). Yi Anyway, there’s rumors about Yi wanting to leave Milwaukee (understandable, since it is so tantalizingly close to CHICAGO!), so perhaps we can obtain him in a trade!!! Does the dream still live?!

Jesse wants Yi on the Bulls!!

The next season shall be interesting indeed!

So today concludes Responsible Conduct in Research week. We did three things - 1) listened to a RATHER BLAND lecture from Colleen Denny about the ethics of human subjects research last Friday, 2) watched AND THE BAND PLAYED ON on Wednesday, and 3) listened to a really strange lecture by Dave McClay about plagiarism and making up data and such.

Now I shall reflect. I think that Colleen’s lecture was informative, but not that interesting. Indeed, it was basically exactly the same as the ethics test they make you take before you do research. Except she didn’t even mention the worst cases of ethics violations - obviously, the JAPANESE EXPERIMENTATION ON THE CHINESE! Tuskegee/Mengele is not even COMPARABLE to Unit 731. Sure, they denied them treatments for syphilis, but the Japs dissected our innocent civilians WHILE THEY WERE ALIVE, without anaesthetics! They also brought anthrax, plague, and tularemia (the dreaded RABBIT FEVER) to our people. The United States barely recognizes this because the Japs SHARED info! GMAFB. Anyhow, enough about that lecture.

And the Band Played On was a little bit interesting. I had to read the book for Patho last year, unfortunately it was a thousand pages. It’s about how the Reagan administration and the CDC didn’t treat the AIDS epidemic seriously because at the time it was a “gay disease.” Well, I’m glad the movie left out the parts about Crisco and stuff, but it was still pretty biased. The ethics violations they wanted us to see mainly concerned Bob Gallo, who stole reagents from the French and pushed his own incorrect hypothesis while the French actually had it right. They portrayed Bob Gallo as an evil dude, but it seems to me like he just wanted some more glory. What’s wrong with that? There were accusations about stealing from the French, but he was acquitted for them. Eventually they determined that it was probably a result of contamination. Overall the movie was pretty interesting though, if a little poorly-made.

The final lecture was a little peculiar. McClay drew a bunch of messed up shapes and asked us to guess what he was trying to say. He drew a red line and after asking us for 5 minutes, he revealed that he was trying to say that “SCIENCE SHOULD TRY TO MAINTAIN A LEVEL PLAYING FIELD.” I highly doubt Socrates envisioned that when he made the Method. He had a couple anecdotes which were interesting, but overall I thought his point was a little obvious. At least it was slightly more interesting than Dr. Denny’s talk.

Well since my project is purely computational, I don’t need to concern myself so deeply with these ethics. As long as I’m careful, I should be fine right? So on to more useful stuff.

So over the last week, as I said before, I’m just ON FIRE. Dr. R finally showed that my code does indeed work! And I read most of they key literature now! So I’m really excited!!!!! Check out the exclamation points!!! I think Dr. R is probably equally excited. I would share the stuff, but I’ll wait until after the chalk talks so y’all will listen. So future plans: over the weekend I hope to practice my chalk talk a few times, read some more interesting stuff (or PODCAST it!), build stuff on Pro/Engineer, and try to finish my C code translation. I think that last part is pretty low priority, I will try to wait until my requested copy of MCell comes in.

Oh yeah one last thing. McClay was talking about how our research experience is enhanced by multi-million dollar machines (it had some loose connection to research ethics). Anyway, basically the only tool I use is the computer. I was pretty jealous of all the people with the PCRs and stuff in their labs at first, but then I realized something. The research isn’t about learning how to use some cool toys, it’s about learning some new stuff, taking down names, making some new ideas, and getting some results. In my lab, I get to think a lot more because my project is a new project, built just for me basically. I don’t work under graduate students, I just think about stuff and listen to Dr. R when he wishes to provide some insight. Basically, this research is my own. That’s my ideal situation, except for I’m worried that I might not be able to get results. If I work really hard, hopefully I can get some result and hopefully publish!

That was a little deep, and pictureless, so I’ll leave you all with a thought from our future Bull:

“MAMBA: I’m about as excited about joining the Bulls as my hero Jason is about doing his research!!!!!!”

So Dr. R’s been back for a while, and we’ve just been going full force. I caught up on a lot of reading, so now I am pretty familiar with the signaling pathways of the neuron. Well, at least a little familiar. I’m sure you all would love to hear about my research, but that’s why you gotta come to the CHALK TALKS! I ran a little presentation over with Dr. R, it actually helped me look back at the bigger picture and see what I’m actually gonna go for. Anyhow, don’t get too excited yet, there’s still chalk talks soon!

My simulation’s also passed a couple of important tests, and I think it is ready to be translated into C. The task is a lot harder than I thought it would be, since all my Matlab code is pretty lazy. But that’s okay, I made my code even faster, believe it or not! I didn’t think it was possible either! The word on the street indicates that C is a hundred times faster, I can’t wait until I actually have it working! All that computer stuff and science stuff made me a little bit curious about genetic algorithms and neural networks. Although it’s not part of my research, I’m gonna look at that stuff soon too! Can’t wait! Don’t tell Dr. R that I’m wasting some of my research time though.

Still a lot of stuff to do, I’ve been doing some MORE readings so that I can know a little bit more. Research is the bizzomb, as the kids say, so I don’t mind. Besides, I still got time to exercise, get a few laughs, and even watch AND THE BAND PLAYED ON!

So stuff to look forward to IN THE NEAR FUTURE: a post about ETHICS (an area that I have never really payed much attention to!) and my reflections on that TOMORROW (don’t worry, I’ve been thinking up stuff!), chalk talks (I probably won’t have the patience to listen to anyone else’s, BUT PAY ATTENTION FOR MINE!), the imminent deal that sends THE MAMBA to Chicago, and the draft that brings YI JIANLIAN also!

My simulation was too slow in the beginning, so I’ve been trying to make it faster. First I thought the only thing that would really work would be to code it all in C, so I started learning that. Then I found some nice Matlab optimization guides. I found a function called “profile,” it is pretty genius! It basically tells me what functions are taking the most time to run and such. After surmounting this obstacle, our hero can get to the really fun part! So far, I made my code twentyfold faster. But it may still need to be even faster, in which case I may eventually have to use the C I learned anyway!

In other news, now that LeBron is LeGone, we can focus our attention to the NINTH PICK IN THE NBA DRAFT. This is when the Chicago Bulls select the next Jordan (or perhaps Scottie Pippen). Who will we get?? Spencer Hawes? Joakim Noah?? YI JIANLIAN?!!

Already in Chicago Bulls red? Already doing it Chi-Town style? Indeed!

Anyway, while you reflect on that I shall recount my own basketball adventures. (That’s right, I’m not HOOKED ON BOOKS). Anyhow I was playing in Wilson against these two people. I could say they were two old dudes that were about 5′11″, but that wouldn’t be any fun. Anyhow, it was like Ben Wallace and Dennis Rodman. Although they were dominating early, our hero would not submit. He finds the ball in his hands at a crucial moment in the game. This could turn it all around! He shoots the three! IT’S GOOD!!! After sustaining a rally in which the HOME TEAM is up by 5 points, Big Ben and Dennis start mounting the comeback. Despite a valiant defensive effort, our young protagonist has found his team down by 1. It’s already game point! He feels the deciding moment, and shoots another three pointer! THIS WOULD BE HIS FOURTH OF THE NIGHT! And it’s GOOD! The crowd goes wild! He rebounds Wallace’s missed shot attempt and brings it out to halfcourt. Then he SELFLESSLY dishes a perfect open shot for his teammate, as the seconds are winding down. It’s … good! And so our hero prevails yet again!

Okay so I finally got around to posting the interview. In the following transcript, I’m D (for “da bomb”) and Dr. R is R (for “R”). Prepare to be enlightened.

D: Tell us a little bit about your background.

R: I grew up in India, in Jaipur. There were a many engineers, doctors and scientists in my family, so I was interested in science at an early age. I did my undergraduate degrees in Physics and Electrical Engineering. I liked my Physics courses a lot more, I applied to the US for graduate school in Physics. I got my Ph.D. in Physics from the University of Notre Dame, and then got a Sloan Fellowship to do postdoctoral research in Theoretical Neuroscience at Brandeis University.

D: Why are you interested in neurobiology?

R: The study of the nervous system is fascinating, because we often see the remarkable examples of behavior everyday, in people, birds, insects etc. As a scientist, you want to explain how these come about. From a theorists’ point of view, the brain is perhaps the richest structure imaginable: a highly interconnected dynamical system that is capable of learning. How do the constituent parts of the brain: the cells and their synapses give rise to behavior is one of the greatest intellectual challenges facing us.

D: Who are some of your heroes/role models?

R: John Hopfield (Princeton): a pioneer in applying mathematical and physical ideas to the study of the brain. He inspired a generation of physicists to enter neurobiology in the 80s and continues to do so today. L. Mahadevan (Harvard) is a remarkable applied mathematician who builds beautiful mathematical models of biological phenomena using fluid dynamics and continuum mechanics to obtain deep insights into cellular function.

D: What is the most exciting thing that has happened in your research?

R: When we confirmed that brain rhythms played an important role in working memory (the kind you need when you have to remember a phone number while you search for a piece of paper to write it down).

D: Did you do research as an undergraduate? If so, how was the experience? Was it similar or dissimilar to what you are doing today?

R: Yes, but this was in a different country (India) where the expectations and the experiences are very different.

D: Describe your research a little bit.

Very fascinating. Now on to me. I’ve been thinking about the project. Right now we’re at the stage of evaluating my diffusion model. I saw this episode of Numb3rs:

If you look closely, you can see the Brownian Motion differential equation!

Anyway, the method I got from it didn’t work that well, but at least I understand a lot more about stochastic processes now. The method indicated that my motion was pretty much Brownian, but I’m not sure if it works exactly how I think it does. Anyway, Dr. R gave me a different way to test it and I built it. It’s running while I blog, hopefully it doesn’t crash.

Finally, the NBA Finals. Although LeBron has lost three games, he will begin the comeback tonight. How can you beat a PHENOM in a seven-game series?! Obviously it’s impossible! LeBron wins four in a row? You heard it here first!

These pictures will answer DMX’s question:

Our hero’s domain.

That corner is the place where I come up with my brilliant ideas.

It’s some other building!

The view’s not bad. I can look far away when I need to refocus my eyes (not like I need to often!) The little people scurrying around often amuse me as well. All in all a nice place.

The lab blackboard.

I forgot to get a picture of Dr. R, so I copied one from the lab website and drew him in. Dr. R says that the lab blackboard is most representative of our lab. I agree, it’s where DREAMS ARE BORN!

OUR HERO!!!

Sorry Justin, it looks like someone already brought sexy back. I’m reading, most likely some math or biology. Reading is good for you, kids.

I also made a lot of progress with my program after strenuously debugging for HOURS, and now I’m learning some more math so I can prove that it’s as awesome as I already know it is. Dr. R’s currently in a conference somewhere, spreading the good word. He wont be back till next week, but THAT’S OKAY, I still got a boatload of learning to do!

NBA update: Although LeBron was unsuccessful in vanquishing the evil Spurs, he still has an opportunity to do so tonight at 9ET! I remember back in elementary school, the best basketball player used to wear all the awesome and1 shirts. Today I saw one, and I thought it would be fitting to share it so we can see how badly LeBron WILL crush the Spurs:

Today in the lab, we (our hero, the Man, and graduate student David) sat down and had a nice discussion in the lab. A lot of new ideas! There’s a lot of stuff that we can try to use the diffusion for, from bacteria fission to the original PSD95 idea. I got a better idea of what was happening. Interesting, yet our hero should be able to get results before the program is over! Indeed, our hero has made great progress this past day. Check it out. Our hero has made the diffusion thing work, it was easier than he HAD EXPECTED! That’s surprising, since rarely does our hero underestimate his abilities.

If that’s not diffusion, I don’t know what is.

Anyhow, I’m working on a different method for diffusion; just “falling off” the edge and continuing down the face. Seems easy right? Alas, ’tis not so! That’s okay, I think I did it. If only my computer would run it. Anyhow, the chosen one shall prevail. Tomorrow I have to get pictures (so say the program people). I know you all are dying to bask in my glory, so I shall get them up soon.

Cavs at Spurs soon. I predict CAVS in SIX! LeBron is the REAL DEAL. Believe the hype. Who do the Spurs have?? Tony Longoria? Tim “Never” Duncan? Manu Ginubili? Robert Whorey?!?! Dubious. WE ARE ALL WITNESSES!!!