It's been more than a month. Studying at Yale has gotten more or less in into a routine of some sort.
Everyday, I will pass by some streets. This is nearing end of summer, where the trees are green and lush. Now it's redder, and the ground littered with dead leaves. But if weather and time permits, you can get your spirits up really by just walking down these picturesque streets...
Physics undergraduate lounge is one of my favorite haunts now. Physics, the bane of my life, is what I mean partly studying now - what an irony huh. Well the lounge when I first saw it, makes me wonder how come I wasn't really attracted to those lounges in NUS... LOLX... They weren't that bad la, but this was different. You have a lounge that overlooks the city, coffeemaker (not free), blackboard and armchairs for relaxing and intellectual discussions on homework and assignments (many people use them really), FREE textbooks to browse through (they probably won't survive the onslaught of NUS students)
Then there's the physics graduate lounge. I kindda like the idea of having blackboards for discussions.
This is one of the chemistry buildings with interesting plaques, with the elements such as Ag, Hg, Au etc engraved on them.
My lunch carts. I couldn't survive without them! Great source of food.
One of my favorite haunts: the medical library. Though it's pretty far off, it's one of the most splendid places to study in. It's like studying in a museum, exhilarating feeling at first, but wears off after you found out you still can't solve that bloody assignment problem. They even have exhibits on display... On retrospect, it kindda looks like the library I saw in Prague.
This is my housemate, M. A nurse-in-training at Yale's nursing school. There's also C, an architect, who is so busy I can't get him to take a photo. But we often have fervent discussions, from pharmocology, clinical talks, genomics, biology to architecture and American politics or just about food LOLX. The picture on the right, is my neighbor's cat. She has these piercing eyes, that follow you wherever you go, clearing the rubbish, walking or stoning or also staring at her. It looked like she is going to scratch you to bits anytime...
Today's biological physics class is extremely exhilarating, despite the fact that I was probably lost half the time, but I could stilll follow some of the equations and treatments that Prof D went. He was extremely fast, so was J, our TA, when he mentioned something and he rattled on like water.
Basically, class today was talking about the contention between entropy and (internal) energy of a system, in order to achieve minimal free energy of a system.
Entropy is loosely defined as the quantification of consistency of certain (micro)states with its meso/macrostates; so by the law of thermodynamics, it increases, OR simply, a measure of the system that you did not know about (ignorance). I shan't go into the treatment of entropy. But here, let me tease apart the energy components that we are defining here. So, free energy here, typically refers to Gibbs' free energy - remember the enzyme energy curve that we always draw in JC, where we are always trying to achieve as negative a delta G as possible, in order for the forward reaction to be driven forward. Loosely put, the resultant products are of lower (internal) energy = more stability than the reactants. In nature generally, things aim to minimize free energy to achieve equilibrium state. In order to do that, we have to apply energy to the system, for the system to do work, in this case, to minimise free energy. You can also see free energy as the amount of energy available to do work (by the system). But free energy is also dependent on entropy as well. To keep things short,
free energy = (internal) energy - temperature * entropy of the system,
where temperature is kept constant
So, contextualising the above physics in a familiar biological scenario: osmotic pressure. Typically, in biology, we name that phenomenon based on the fact that there is a pressure exerted (on a semipermeable membrane) by the solutes in a solution against the inward flow of water/solvent, due to osmosis. Imagine we have our standard osmotic pressure experiment, where we have a box, divided into 2 sections by a semi-permeable membrane. In one section of V volume, you place N molecules in it. To keep this concentration of solutes in place, work has to be done by the system to keep the solutes from moving out too and this corresponds to the amount of free energy available to do work. And using the free energy equation above, if we assume all the solutes to be ideal solutes (which is like ideal gas assumption, where each particle is pointlike, totally random and non-interacting), the "internal energy" of the system as a whole can be ignored. Work done is also defined by the pressure * volume, so to counteract the water moving in, work done by the solute = the osmotic pressure * volume occupied by each solute. If you can imagine, then the amount of work done which is dependent on your free energy (to do work) per unit volume would correspond to your osmotic potential, which after a semi-long mathematical treatment, would give you:
osmotic potential = n * K (Boltzmann constant) * T
I do not know about you, but when I saw that, the IMMEDIATE thing that came to mind, was the equation of the ideal gas, pV = nRT (and I am surprised myself how fast that came, considering the last time I used that was, like 10 years ago!!)! And it turns out, it IS the ideal gas equation, since n in the ideal gas refers to number in moles!
SO, long story short, the conclusion was that osmotic pressure AND ideal gas pressure are really forces that a system exerts in its attempt to increase its entropy (2nd law of thermodynamics). Contrast these mechanical systems (where no energy assumed due to idealized particles) with a simple mechanical system, of a spring, where no entropy is involved, only aim was to reduce the free energy, you end up with a entropy-energy spectrum representing all situations, where in real-life situations, systems are really in the intermediates, a competition between minimizing energy and maximising entropy to obtain an optimal minimum free energy state.
Prof D ended the class with an analogy from amoeba being placed in pure water. In high-school biology, we often viewed that as a proof of osmosis in hypotonic solution, where the amoeba eventually burgeons (and explodes if left too long) when the cell semipermeable membrane cannot withstand the rapid increase in volume. But if you look at it in the physical point of view, the law of thermodynamics in entropy is STILL a universal governing law! In fact, the solutes is trying to get out of the amoeba, IN ADDITION TO, the water getting into the amoeba!
I couldn't find a good "bursting" experiment video, this is the best I could find on YouTube for RBC: not that great IMO LOLX
It's mid-autumn festival. The moon is still round on the other side of the globe...
Last Saturday, I met up with a postdoc from AP's lab (a structural biology lab), DH. He is from China but he studied at NTU in Singapore, and before I came over Yale, he willingly helped me with some questions. Extremely helpful and friendly =). He even picked the tab for my lunch that day!! Thank you so much!! It was then I also realised he just arrived in May this year too!! Hmmm, I do not know what you guys think, doesn't DH look like a Japanese?
So, having not tried the famed Miya's restaurant, we decided to hop on down there for lunch. Miya's restaurant is a fusion sushi restaurant, that is supposedly the best in Connecticut and the third best in the whole of USA. But alas, I have come to doubt the subjectivity of the American taste in the face of Asian cuisine, so I have decided to try it myself, dragging DH along with me...
Miya's is located on Howe's Street in New Haven, sequestered away in a quiet neighborhood, just a stone's throw from Broadway. Fortunately, we came early for lunch, there was no queue. One side of the restaurant seemed to be booked for photoshoot though! Anyway, the waiters were all very nice and helpful and that particular one (in the pic) who served us had a good grasp of all the ingredients of the sushi. I was impressed indeed, because all the sushi, are fusion, and definitely not made up of minimal or the normal ingredients, like the ones in Singapore, or those authentic from Japan (which I haven't tried).
Pumpkin soup on the house
We couldn't make up our mind, so we ordered each a palette of sushis that showcase the different array of sushis they have: funkily called "a very hungry inch worm" and "bleu plate especial". BTW, they all have funky names which I couldn't remember LOLX. Taste-wise, not all tinkled my tastebuds the right way: there was the chocolate one which I thought should taste better without the soya-sauce-taste (I am not a big fan). I have tried the sweet potato one, which just isn't my cup of tea. But I am thrilled over the sushi with a tart crust surrounding the rice. It's not like the sushi is sitting in it, but the crust is part of the sushi. That tasted exquisite and exotic, for a sushi lover like me. One common thing I observed, was that they stuffed lots of things into each sushi; at least 3 or 4 ingredients in one single sushi, which is definitely something rare or even unheard of in Singapore. So the next time you guys come over to New Haven, and are looking for some taste-bud adventure, try Miya's sushi delight. You would be in for both surprises and disappointments, but that's how adventures work, isn't it?
As I try to do the balancing act of course-taking, lab rotation, my-own-time and XL-family-time, just thought it would be nice to update nice once in a while. Blogging kindda sets things in perspective I guess. So I have finally found myself a lab in my first rotation: Lynne Regan's lab. Prof Regan has some awesome projects, but most notably and what her lab is known for, is TPRs: tetratri-copeptide (short description); it's such a niche area of research that I can't even find it on Wikipedia!! LOLX.. landmark paper here...
If you look at the diagram (number c), you can imagine each TPR as one module of the same color (red, yellow, blue). So you have there 3 and half (the green segment) stacked in a spiral manner. Each of these 3 TPRs are similar in length and sequence; so you can imagine LEGOs of similar size stacked up. The minimum binding unit is apparently a combination of 3 TPRs in tandem. So the Regan Lab has done much on TPRs: elucidating their structure, consensus sequence, their binding specificities and partners, functions and implications in certain diseases. One of the things they are moving into now is the applications of these TPRs.
As you can imagine, one of the most obvious applications, by virtue of the LEGO-like repeated motifs, is the synthesis of artificial peptides. Unlike most other proteins, which are globular, where you cannot easily just stack up parts of the proteins to form a larger one, TPRs can be synthetically engineered to have competitive functions to naturally occurring peptides, particularly antibodies, to aid in inhibiting pathways that lead to diseases, say HIV in AIDS or using the TPRs design as anticancer drugs. This could be my small step into the realm of synthetic biology that I am really trying to get a handle on...
So that's my life as of now, other than MATLAB, biological physics and biomedical informatics, taking up the bulk of my life...
But anyway, just to catch up on events. On Labor Day (US it's on Sept 6th), there was Stratton Faxon New Haven Race. Apparently, it's in its 31st year. Just 3 weeks here, and I embarked on my first ever running event at New Haven. Sweet =)
Prof Regan "invited" me to run (I had to pay on that day -_-|||, which is more expensive btw), but I got this great T-shirt that she made for her lab!! Thanks! And of course, I enjoyed the run very much. I ran 5km in 28 min. Think that's pretty decent =) And seriously, the weather was good, sunny yet cooling. It was pretty well-organized for its scale (not very big compared to those in Singapore). So I would say I would enter again next year. Just to keep myself in the keeping-fit mode. Photos as usual, on facebook =) A pity though, G and M didn't get to take pictures with us.
What is the most resilient parasite? Bacteria? A virus? An intestinal worm? An idea. Resilient... highly contagious. Once an idea has taken hold of the brain it's almost impossible to eradicate. An idea that is fully formed - fully understood - that sticks; right in there somewhere.
As life propelled into the the school year full steam, I feel myself leaving lots of memories behind without really sorting them out and looking at them a second time. As D aptly put it, "discombobulation" =) I am heeding G's advice and putting DMV behind (at least until I got all the necessary stuff) and plunging head-first (bad position) into assignments, presentations and lab rotations (which I haven't really decided)... (For more pics, go facebook)
Fall semester officially started on the 1st Sept. Like NUS, they have a "shopping" period, but unlike NUS, you actually get to add the course information to your schedule (or an IVLE equivalent - classes*v2) first, then when you have finally decided, just drop those courses you do not want. The final decision has to be sent to your prof-in-charge via another enrolment webpage. So you have the status of a "shopper" for 2 weeks, till 15th Sept - hence my hectic shopping list. In the end, I ended up with 2.5 courses, and auditing for one more. The other difference is the idea of auditing, in which you are labeled an "auditor", appears in your transcript but not graded. So it depends on the lecturer how much she/he wants you to participate. I think this is a damn cool feature! But I don't like the fact you have to register on 2 sites instead of a combined one - it makes things very confusing sometimes, and somewhat lacks organization.
Our CBB seniors also gave us a treat at C's place. His place is gorgeous!! But probably pricey too... New Haven is said to be famous for its pizzas and hamburgers, Miya's Sushi. So we had pizzas during the senior-treat-junior session. And boy, our seniors can really talk... The whole discussion about profs, labs and courses were mainly dominated by them but it was REALLY informative =) and funny (especially those parts about some of the pet peeves and the behaviour of profs LOLX)... And I realised, all of them have a very strong rapport and camaraderie forged; no matter which year they are from. And... I do envy that... Hopefully, we will grow to become like that too.
Saturday afternoon was spent at touring New Haven and spending some time at balmy and green East Rock Park. It's called East Rock, literally because it is a park on a rock that is formed in the eastern side of New Haven... This is the first time I am there, and I took a liking for it immediately. From East Rock Park, you could see almost the whole of New Haven. People were picnicking and frolicking in the meadowlike greens. Nice weather too, despite Hurricane Earl.
Before my next appointment, I had some time in between. So I decided to sit down at some cafe and do people-watching (or being watched -_-|||). Blue State Coffee cafe's coffee machines ALL broke down... Win liaoz lo... So, I decided to try Ashley's ice cream, claimed to be the best in Connecticut. It wasn't too bad, just that I find the butterscotch too sweet for me. XL might like the ice cream though =)
Saturday evening was with the MASA (Malaysian And Singaporean Association) at Basil Restaurant, which is this Asian restaurant near Broadway. I didn't know there were so many Singaporeans and Malaysians at Yale!! Almost the entire restaurant was filled! Apparently this is the first time there is such a large turnout. Most of them, are undergrads and professional school students. I really like that fact that I get to speak Singlish again haha. Also what I like most about the interactions, is that there are really lots of interesting stories to listen to. So hopefully we will meet again =)
And that was the first time I took the night shuttle back to my apartment; they actually bring you straight back to your apartment from any point in campus. Refreshing experience.
Second time I was turned away from DMV but the three and a half times I have been. Please do not ask me about the half time.
Just for record purposes, and for those of you intending to come to US for studies or work or are here but haven't tasted DMV yet, the following documents are required at DMV:
Primary ID documents (more like a package)
1) Passport with correct VISA
2) with I94
(one of THE most important things to identify you as a LEGAL resident in the US, an entry card from the Homeland Security, you must write this when you are on the plane flying here...)
3) I20
(official University acceptance, issued by the International Office)
4) University International Office letter, preferably with an embossed seal, or any form of identification that you are working/studying here and signed in a color other than black (haha, this is from G. She had this incident when she was sent back because the letter was signed in black and the DMV person thought it was photocopied *faint* and she had L signed in RED LOLX)
5) Social security denial letter, evidently from the Social Security Office, stating that even though you were denied number, it does not mean you are ineligible for it; the SSO people also lambasted DMV...
6) A letter postmarked, meaning it has to be from the US post office; the letter that was sent to your place by the bank with your debit/credit card doesn't count but surprisingly, the bank statements count. And the DMV peeps actually found that sending postcards/letters to yourself seemed more credible than a mail sent from the bank with your debit/credit card in it.
Secondary form of ID (to further verify you are REALLY you *pinch yourself*)
7) Transcript. Since you will probably just arrive in US, the school will not have a transcript for you or if you are working, you won't have one anyway. I didn't bring mine from NUS. But thankfully it will be in English anyway, otherwise, you would need a LOCAL VERIFIED US translator (UK, where English originated from or Australian not allowed apparently) to convert the transcript language to English.
So, well please be prepared to be sent back a few times.
And to complete this record, something not related to DMV, but the US immigration has imposed a new ruling when I flew from Singapore. Some online electronic system for travel authorization. Even for countries like Singapore, under the Visa Waiver Program. Now even when you travel to the US for a short period of time, you will still need this since it will give you a number that they will verify. A Very trivial, but sure scared the shit out of me when I was at T3. Nobody told me anything about that until this.
I think they did this on purpose. It wasn't even specified hat we need to APPLY for the class. Ok, not that I did ask for the venue when it wasn't posted online... *bleah* So hopefully he is still teaching in the coming semesters..
Conceptualizing obstacles and opportunities in international relations with an emphasis on the strategic utilization of military and diplomatic resources. Through a series of lectures and interactive forums, students will be encouraged to learn how to keep their freakin' mouths shut."
http://www.huffingtonpost.com/2010/08/16/stanley-mcchrystal-yale_n_682960.html "At Yale, McChrystal will possibly join the ranks of other high-profile faculty at the institute, including former Mexican President Ernesto Zedillo and former Deputy Secretary of State John Negroponte. According to the Yale Daily News, Yale President Richard Levin said that "bringing more people with experience in international affairs" was a "priority" of the center."
BBS orientation was held at The Anlyan Center (TAC), in the medical school campus. As usual, Yale feeds us very well. Apparently, we have free food at almost every single event! Please don't get me wrong, I am NOT complaining =) But, I am guessing the main idea of such is for socializing purposes. Such is common in Singapore too, but people seldom use the opportunity to interact, that's all.
So, we started with breakfast (myriad of breads and cordials). In the midst of eating, I met up with my CBB group for the first time! Our registrar, LS, was oozing with motherly love, and I immediately took a liking for her. I got to know too that despite there were only 7 of us, it was already considered a large class (previous years were really small that is).
Prof J. Alv kickstarted the orientation with Prof L. Cool., our BBS director. I particularly like the "OSMOSIS" information booklet. Aptly named of the supposedly natural physical process that is required to absorb (but very so often eluded us :S). But "ACTIVE TRANSPORT" might prove to be more apropos of the ACTUAL process.
Subsequently, we met our direct CBB senior, Dan, who gave us a tour of some of the more relevant facilities of the medical campus. This ended with lunch at the Graduate Club, which is this posh-looking Victorian (??) "private membership club est 1982". Check out the spread! If just looking at those make you drool, really, imagine being there! XL will swoon over the pastries LOLX!
It was really cool to meet everyone for the very first time. Some of them seemed so young!! (o.o||| Also, found out then G just got engaged =) Congrats once again!! Hopefully, we will all build a great camaraderie and friendship.
Apparently NUS AlumniMail has undergone some revamp. And now, you have to log in to https://www.alumni.nus.edu.sg/alumNET/groups/contactlist.jsp to log in and set up an Windows Live App alumni email account. In order to consolidate onto your own Outlook though, the servers have changed:
Alumni mailboxes lend some credibility to the emails you are sending out. So mailboxes from recognised universities are some of the best resources you have; also nowadays you can gain access to a wealth of information and contacts from the networks from Facebook LOLX.
A question posed by Prof Miller during class today.
Options:
A) Within many different individual bioscience and clinical departments?
B) In its own department
C) In a computing support unit?
What do you guys think?
Although this question seemed more for hospitals and perhaps academic institutions, it occurred to me it can apply to a more general research setting - research institutes, even other drug/pharmaceutical companies too. And it happens that it seemed to be able to be applied to my ex-job at Genome Institute of Singapore (GIS). If you think about it, RCG is like a biomedical informatics group, with people doing a myriad of different biomedical informatics - sequencing, population genetics, maintaining and creating applicational tools and database management for biologists and webpage and software mediation for the institute as a whole. It IS a support unit, on the institute's point of view, but yet functions as an individual department. And, if you think about my friend Ri in Mark's lab (I will want to believe he has a team of bioinfo guys now haha, but then he might still be outsourcing hehe, which isn't exactly a bad thing) previously or the bioinformatics specialists recruited to the different labs, you can also imagine a one-person support unit within the bioscience department or group.
The answer to the question will have to depend on the needs of the center. A center that is organized into labs, and heavily relies on computational technologies would necessarily require bioinformatics personnel in their own departments, in which themselves will have their own needs. And if the center is large enough, a new department can be established, to act as a home-base for additional personnel and it can serve both as an autonomous entity, with its own managerial and administrative arrangements and/or a consultancy firm of sorts, and also a common resource pool that everybody in the center can tap into. Such could relieve budgets on the individual departments and consolidate manpower, and allow development of the individuals that join the biomedical informatics department. So, suddenly, I am in awe of GIS (or maybe just Ed's or Guilliame's) foresight in putting together such a department in the first place =)
I do not think it should be a computing support unit, but rather a biocomputing support unit. If it just involves simply building IT infrastructure with no biological or clinical relevance, then this ought to be a separate group altogether. But then again, if the center is not that big enough, they could be integrated too.
Outside the academic center, however, biomedical informatics organization would probably act as a consultancy and/or educational firm or quite a buzz thing in Singapore now - contract-based. Much like CROs (contract research organizations such as Quintiles or Kendle) or just intermediaries that other organizations/research institutes/academic centers can outsource their work to (like Beijing Genomics Institute for very large scale sequencing and bioinformatics analyses).
You can also look at these options in order of their importance. I would deem the role of biomedical informatics as (A) be most important, followed by (B) and (C). So a center can acquire these resources in this order as they grow.
So, if you are getting the drift, basically, relevance is the key to deciding which is more beneficial to the center's organization of resources. Choices are relative to the needs and demands of the institution.
I think I articulated really badly that day... Kind of convoluted... But I will improve on that! =)
It's been more than a month. Studying at Yale has gotten more or less in into a routine of some sort.
