Only Breath

Harvard Immunology Recruitment 2012

2012-01-23T11:00:00.003-05:00

It's very odd being a third-year and realizing how old you feel at the recruitment dinners and house parties (even if there's a chance that the recruits are the same age or older than you). I remember that at one of these recruitments, I met a fourth-year student and said, "Oh wow, G4 -- that means you're almost done!", to which the G4 was courteous enough to just smile and say, "Mhmm, yeah....sort of!"

I have to give that G4 a lot of credit because if it were me on a crabby day, I might have punched someone in the face. Bitter G3s will know that I might not really be kidding about that.

KA-POW!

Another funny thing that happens for me is that there is always one recruit who asks if I have a blog. This stems from the fact that somehow, Google has ranked my immunology blog post from when I interviewed in 2009 pretty high up among the results when people google "Harvard Immunology Recruitment." I have to say it's pretty flattering for me, even if it's of no credit to me. (Well, at least we didn't have to put in the effort to Google-bomb it up a few rankings.)

I'll just relate something of interest to me that happened during the recruitment. I was asked what made me choose the Harvard Immunology program over the other programs to which I was offered admission. To be honest, as the years pass (and I made my decision in the winter of 2009), I can't really remember what went through my mind as I made my decision. It was pretty hard. I did know that I really wanted to go to the Harvard Immunology Graduate Program ever since I started attending the Wednesday Immunology Seminars (which you all should make a point to go to, even as you see the upper years' attendance dwindling!)

I don't know if I had any legitimate reasons for choosing Harvard Immunology over other programs. In retrospect, I really appreciated a few things about Harvard Immunology:

1) The fact that there is some flexibility for rotating in and joining a non-immunology biology lab. I've joined a genetics lab that works on host-pathogens interactions and I know other people in my program who have rotated and joined labs that are more related to microbiology, virology, neurobiology, molecular biology/genomics -- you name it. It's possible.

And let's face it, sometimes our interests change, and that can be a really good thing. When I joined the program, I thought I was absolutely set on working on Th17 and Treg cells (I really thought they were the sh_t because they were, especially in 2007 when I was first attending the immunology seminars). Then when I started attending classes, I thought I was absolutely set on working on the gut microbiota and its role in modulating host immunity (also the sh_t, and still is). I rotated in a lab working on exactly that, another lab that worked on DNA repair and translocations (for one summer, I worked on AID), and a third lab that was out in left field: it worked on C. elegans as a model for innate immunity. It was a lab that I couldn't even believe I was thinking of rotating in, just because it was so far from what my initial interests were! Moreover, I rotated in the lab at the behest of my graduate student mentor: somehow he thought the lab was quite cool (I thought it was absolutely ridiculous). Do you know what happened in the end?

I joined the C. elegans lab. (I'll post about that some other time.)

I work on this thing. Scanning electron microscopy makes everything look freaky.

The point is that many of these choices are purely serendipitous in the end and sometimes unpredictable. I had great rotations and when I finally narrowed it down to two labs, I nearly ripped my hair out trying to make the decision. It was a very "gut feeling" (no pun intended, honestly!) when I finally did choose the C. elegans lab, and while it's only been a year and change of being in the lab, I'm still glad I made the decision I did.

2) Boston being extremely close to a number of other great institutions. I go to seminars at Harvard University (yes, it really is a bit different from Harvard Medical School) for microbiology, MIT (my alma mater, but they have some good molecular biology talks and I'm still on some email lists from them - the Whitehead and the Broad are a stone's throw away), and since I'm now more into microbiology, it's good that I stayed in Boston: Tufts Microbiology is also a great program and at the Boston Bacterial Meeting, I learned that Northeastern has some good groups also interested in high-throughput screening for antimicrobials.

Boston is certainly an exciting city to be in, especially if you're a biologist. For the density and power of the institutions, I am pretty sure you will not find it anywhere else in the country. I've even heard post-docs who have been in Boston forever lament when they end up taking a job outside Boston. If you take advantage of what Boston has to offer for biology (the academics, the talks/seminars, the classes you can cross-reg for, etc.), you're going to miss Boston when you leave it.

3) As for the other things, I'd be happy to tell you in-person. :)

So here's the last bit of the post:

Dear Harvard Immunology Recruits of 2012,

You all seem like awesome and cool people. I hope I got a chance to meet you during recruitment, but if I didn't, I hope I will see you again -- hopefully as the upcoming class of 2012. Best of luck for your future interviews and I'm sure you'll have plenty of good options to choose from in the end.

Thymocyte

(And if you join, you can give me more ideas about LOLcat-type immunology images!)

Dear MIT

2011-12-09T15:18:00.001-05:00

Dear MIT,

This is the one time where I am absolutely PISSED with you. Normally, I'm very proud to wear my brass rat everywhere, sport my MIT shirts wherever I go (to the dismay of all my lab members), and remind people of where I did my undergrad.

But sorry, not this time.

I wasn't happy when Governor Deval Patrick became our commencement speaker in 2009. In 2008, at least the kids got Muhammad Yunus. I understand that you don't want to flake out (being MIT and trying to live up to your prestigious tech school reputation), which is why you don't choose J.K. Rowling or Oprah. But seriously, Deval Patrick?

I took solace in the fact that the commencement speaker of 2011 (Ursula Burns) was just "okay".

What I wanted to know is, What the HECK happened this year when you finally shaped up, finally got your act together and got Sal Khan (of Khan Academy fame) to give the commencement talk? First, it's about time that you started getting some more sane and inspiring people (read: not Ben Bernanke, not Bill Clinton, not Deval Patrick...) and finally picked someone that:

1) The MIT students could relate to (I mean, he's 35! He uses YouTube! He knows its power!),
2) The MIT community should be deeply inspired by, and
3) Is not screwing the state or country, for that matter.

Of course, #3 applies to the three individuals I've named and obviously not Ray Stata and a few others. And no pun intended on the italicized word in #3.

So, MIT, it's finally ABOUT TIME that you picked someone sane, but I'm NOT forgiving you for being so late in making such a change. You're at least three years late.

And for that, I guess I'll just have to make it up by crashing this year's commencement to hear Sal Khan speak.

>:)

Sincerely,

The Angry Thymocyte

Satan's new pasttime: inducing anaphylaxis?

2011-10-26T12:07:00.004-04:00

Believe it or not, I'm usually not very outspoken about my religious beliefs, as I believe it's a very personal belief. For me, it's a combination of many thoughts I've been brought up with, as well as many ideas that I have encountered recently. Furthermore, as someone recently reminded me (who herself is a sort of agnostic/theist), religious beliefs do change over time and are reflective of an individual's personal journey through life.

That said, I'm going to open my mouth and rant about something that I found in my inbox, which made me want to scream some expletives, grab the nearest heavy (and heave-able) object, and throw it out of my lab's 7th floor window.

It has to do with this email, which came to us from the pastor of my parents' church. He posted the original email on his blog (names unredacted) and it can be found here in a post called "Prayers Needed Part 3". In it, our pastor (who I will say is a concerned and very nice guy) talks about the uncannily and "uncoincidental" epidemic of near-fatal allergic reactions experienced by some of the church members, which he realized after he and his family were in a car accident, where no one was critically injured.

After reading his email, this is what I concluded:

First, it is sad to hear that some church members had such severe allergic attacks, since anaphylaxis can be fatal, but I sure as HECK do not think that Satan is putting nuts and shrimp into their food. Or messing with allergen:IgE binding kinetics.

Although I'm no immunologist (I work on host-pathogen interactions in a small, cute nematode), it is not bizarre for people who have severe food allergies, like Benny, to have reoccurrences when they are older, although some people do "grow out" of it. I don't think that these people have sinned more to get these allergic attacks and I CERTAINLY don't think that Satan is specifically out to get these people. I heard that recently, our pastor has been saying that all this changing weather has been indicative/suggestive of the end of the world. I think that what is far more disturbing than the end of the world is when people exaggerate small, but unfortunate events and attribute them to much larger forces.

For instance, why was the pastor's interpretation of the event not, "So-and-so had a near-fatal anaphylactic shock. Praise God that he's okay!" Then we could easily ask "what about the people who actually die from the allergic reaction? Was that just Satan's doing?"

Let's assume (though I've forgotten enough immunology to say how much of a basis there is for this) that allergic reactions are dose-dependent and also dependent on a person's sensitivity. For instance, some people who are allergic to animal dander can go into anaphylaxis even if the animal is quite a distance away -- it depends on the air ventilation in the room. I knew a professor who went into anaphylaxis when a lab member accidentally brought a mouse into the lab and she had to be taken to the ER. Does that mean that Satan is also dose-dependent? Does Satan sometimes directly correlate with the amount of allergen present?

Why couldn't our pastor instead have reasoned that despite the seemingly uncanny nature of this chain of events, it may be simply probabilistic? For instance, take this completely imaginary conversation (though two of the situations are true):

Thymocyte: "Two years ago, I went to In-and-Out Burger and got food poisoning. Must have been a bad patty."

Thymocyte's thesis advisor: "That's terrible. Actually, my daughter a few days ago wasn't feeling very well. It turned out after eating all those spicy chillies at the Sichuan restaurant we went to, she had some bad diarrhea."

Thymocyte: "Sorry to hear that, hope she's feeling better. Spicy food does increase gastrointestinal mobility. But come to think of it, one of the post-docs in the lab had food poisoning at the worm meeting in UCLA!"

Thesis advisor: "Oh yeah, turkey sandwiches, that's right. He isn't the only person I've heard who had food poisoning from a turkey sandwich. In fact, my wife was eating a turkey sandwich on our trip to visit her father when -- "

You can see two things.

(1) Every account of a really bad, upset stomach was accounted for by a specific, causative agent. In three of the examples, it was likely bacterial growth in the food that led to food poisoning. In another case, it was just spicy food, which many of you know leads to firerrhea (if not, I encourage you to eat a plate full of Spicy Sichuan Peppercorn Chicken.

Fire-rrhea is guaranteed or your money back!

How did the bacteria get in there in the first place? Someone may say Satan ("Look how many people we just named who had food poisoning within the past months, isn't that inexplicable???") but I would say that some fast food joints just need to get their act together and throw out old food. Dehydration can potentially be fatal, so why don't we attribute this to Satan's doing here?

If we accept that dehydration from untreated, serious diarrhea can be fatal (which is true), then why don't we say that Satan specifically targets third-world countries, where there often isn't clean water? Wouldn't it be much more reasonable to simply attribute death from untreated dysentery to a specific microorganism (Shigella and Entamoeba, among others), which is the result of mismanagement of a country's resources, lack of available antibiotics, bad economies, and faulty governments? Or should we just say "Satan just has an extra vendetta against poor nations"? It's because it doesn't make any sense at all.

(2) My other point is that sometimes when you have a conversation with another person about a topic, both parties will probably reminisce and start listing (in their head) everyone they remember who has had similar symptoms. We have just named four people who encountered bad stomach trouble "recently" in this made-up, but equally plausible conversation (me, my advisor's daughter, my advisor's wife, and a post-doc in the lab). This is still much more uncanny than our pastor's example (he only named three people with allergies, mentioned one person who asked him for prayers for our college group, and our pastor alluded to his recent car-accident). In fact, I actually know two other real cases of people who have been having gastric problems recently, both who are immunologists! If we add them into the pretend-conversation, does that mean Satan has a vendetta against the people who works on the immune system?

I'm not saying that Satan doesn't exist. If Satan is the originator and/or epitome of evil, just looking around will tell you that there is tons of evil in the world. Don't we see it every day when we hear about young people getting killed by a drunk driver, war atrocities and crimes (read a young woman's account of a rape and you will certainly feel your heart being torn apart), or even monetary inflation and how it is only aggravating poverty (see this story to understand what it means to be impoverished)?

Maybe Satan is simply a metaphor for the sum total of all our failures and inadequacies as humans.

Our pastor is a good guy, but it is critical here to think again about what to call an example of "present darkness" and "spiritual forces of evil." The belief that these events are directly related to the supernatural would set us back as sentient, rational beings and reduce us to silly superstition.

Let's call and allergen only an allergen and nothing more.

A most beautiful realization

2011-08-18T17:05:00.000-04:00

During the time when I freaked out and realized that I was a pauper, I signed up for a lot of stupid things that were probably not worth their time, but generated easy money for me.

No, not that sort of thing. They were namely psychology experiments that were extremely boring and out-of-the-way, but some of them were actually voluntary blood draws.

One of them, relating to ulcerative colitis, required me to call their office. I really hate calling people on the phone for business-related things because:

(1) I can barely figure out what some people are trying to say to me over the phone. Why do some people speak a mile a minute?

(2) I think I'm extremely awkward on the phone because I'm generally bad at things that I cannot do pre-meditated. (No, not like that, either.)

Anyway, so I did call the office of this certain study and said that I was interested in learning how to be a volunteer for the study. The man asked how old I was, and I told him I was 23 years old, and he confirmed that I was female. He then said he wasn't sure if they needed more volunteers, so he put me on a very short "hold" and went to check the logs.

When he came back, he said, "Yeah, I'm sorry. I don't think we need anymore Caucasian, female volunteers in the 18-23 [year-old] category..."

Of course, I replied: "Oh, but I'm not Caucasian ."

With shock in his voice, he said, "OH! You're not???"

And I said, "No, I'm not. I'm...Asian-American."

...to which, he said, "Oh, that changes everything! Let me go back to look at the log, I'm sorry about that."

Now, this event seems rather banal to most people and would garner, at most, a chuckle from people. However, this was an AMAZING moment for me. It was when I realized that on the phone, there is less (visual) prejudice, simply because people can't place my ethnicity by just hearing my voice -- to them, I have an American accent, and that's where it ends!

(...though I've been told on multiple occasions that I sound like I may have been born in Singapore or Hong Kong, based on an odd twang I've acquired, and perhaps not enunciating as well as I really should.)

I know this sounds weird that I'm emphasizing this point, but it's weird (especially being an Asian-American who admittedly speaks crap Chinese -- Rebecca Wallace may even speak better Chinese that I do) when you go through life with people forming strange ideas and opinions of you, just based on a minute talking to someone who is ethnically of Asian descent.

For instance, I recently moved into a place in East Boston. The girl subletting her room to me is East Boston -- born and bred -- and was pretty nice and accommodating when getting me to rent her room. At some point, she asked where I was from.

This is the classical question that Asian-Americans get that can be so hard to answer. It can be answered in some several hundred ways, and is highly dependent on who asks you. Here are some scenarios.

I am asked...

(1) ...by a Chinese post-doc in the lab.

Post-doc: "Hi."
Timocita: "Hello!"
Post-doc: "Are you Chinese?"
Timocita: "I am....well, my parents are, but I was born here."
Post-doc: "Oh, so you don't speak Chinese?"
Timocita: "Not very well, no. I'm sorry."
Post-doc: "Oh." [Walks away, disappointed.]

(2) ....by Southwest Jiaotong University students on a tour of MIT and Harvard that I am giving (in English, of course.)

Student: "Hiiiiiiiii, do you speak Chinese?"
Timocita: "Urr, not very well, no."
Student: "No??? Why don't you speak Chinese?"
Timocita, a bit defensively: "That is actually a very interesting question. I guess I can answer it a few ways. One reason why is that many American-born Chinese who do speak Chinese well were raised by their grandparents. I wasn't. I was raised by my mom, who came to the U.S. when she was 11."
Student: "....sorry!? I don't understand."
Teacher: "You need to improve your English."
Student: "Huh?"
Teacher: "I said you need to IMPROVE your English!"
Student: "我听不懂..." [Chinese: "I heard it, but I didn't understand..."]
Teacher: "我說你應該提高你的英文!!!!" [Chinese: "I said you need to improve your English!!!"]

It was amusing then but yes, on that tour, there was a wide range of English proficiency levels -- from extremely good to 'state of confusion'.

(3) ...by a new, enthusiastic Chinese acquaintance.

Girl: "Hi, do you speak Chinese?"
Timocita: "Not quite, no."
Girl: "But are you Chinese?"
Timocita: "I am. I mean, my parents are from Guangdong, but I was born here."
Girl: "Oh, so you speak Cantonese?"
Timocita: "Well, a little, but it's not so good."
Girl (in Cantonese): "你識唔識講廣東話?" ["Can you speak Cantonese?"]
Timocita (in Cantonese): "我識聽一啲,但係唔好識講..." ["I can understand a little, but I don't really know how to speak..."]
Girl: "We can practice then!"
Timocita, cringing: "But....I actually don't know how to compose sentences...."
Girl: "How can you not...?"
Timocita: "When my parents speak to me in Cantonese, I usually respond in English...but nowadays, they speak to each other in English."
Girl: "O____o;;;"

It sort of ended there. And yes, I really don't know how to compose sentences.

(4) ...by East Boston soon-to-be-housemate, who was subletting a room to me.

Woman: "So, where are you from?"
Timocita: "Well, I'm originally from Long Island, New York...but my parents are from southern China and all my family is in the U.S. now."
Woman: "Oh, I see. So you were born in the U.S.?"
Timocita: "Yes."
[Later]
Woman: "So here's the bed. It's a full size. And this futon pulls out to be a bed, so you know, if you have friends or family from China coming to visit you, they can crash here."
Timocita: "-_- Thanks."

I mean, she meant it in a nice way, but the comment rather unnecessary...especially the specification that they would be from China. I probably have more friends who live in France than in China.

When I told this story to someone in my lab, he said, "Well, at least she didn't say 'When you gigantic family from China comes to visit you'!"

I suppose so, though there is that ONE CHILD POLICY.

(Anyway, never mind.)

You do, however, find some Asian-Americans who despise this question and go out of their way to torturing the questioner. I have heard some Chinese-Americans claim that they were Hawaiian when they were asked whether they were Chinese, just because they hated having to explain their whole life story and justify the gravest sin in their life: not speaking fluent Chinese.

Some Asian-Americans I know even have some major identity crises, even hating all things related to"Asian" culture, saying repeatedly that they are not sexually-attracted to Asian women (which is a personal preference, so who knows), and only choosing "American" to identify themselves.

I guess it can be tough, depending on where you are on the sliding ABC scale.

On the term "American-born Chinese," which I was amused by:

"However, this sort of categorization oversimplifies the social realities and identities of many Chinese-Americans. It is often overlooked that innumerable Chinese-Americans are still connected to their parents' heritage, and it perhaps too quickly valorizes an attachment to an ancestor culture in favor of assimilation and integration within a new one."

Also: "Asian Americans often report being asked the question, 'Where are you really from?' by other Americans, regardless of how long they or their ancestors have lived in United States."

An accurate answer?

"Africa."

Lessons from the pGU's guru

2011-08-16T11:34:00.007-04:00

Some of you may remember a certain Taiwanese post-doc that I used to write about in my past life in my undergrad lab at MIT. Just because he'd probably like to maintain a bit more privacy than what I'd like to offer him, I will refer to him as "Qinghong," which would be what his name would be in pinyin.

This morning, as I was lifting a rather heavy centrifuge rotor, I was thinking about something Qinghong told me three years ago.

There was one day at the MIT lab that I needed to bring down a carboy filled with some buffer (TAE or TBE) from a very high place in the lab. In case some of you were wondering what the heck a carboy is (yeah, I realize it's a strange word), here is a picture:

Yes, this took me much longer to make than you'd imagine...with plenty of lab folks passing by and wondering what the heck I was doing.

The carboy that puny undergrad Thymocyte was trying to bring down was quite heavy -- it might have been 15 gallons or more, and either way, I wasn't able to do it, even with a step stool. I was going to ask the pGU for help when Qinghong told me about his former PI in grad school.

Qinghong's former PI was a woman and had some very firm, somewhat feminist views. She would not allow the female lab members (this was really only a concern for them, actually, as you can imagine) to ask another lab member (usually male) to help them lift something heavy. Yes, all the heavy, unpleasant, painful manual labor had to be done by the female lab member and the female lab member alone. She had to just grit her teeth and do it herself. And some rotors can be more than 40 lbs (which always feel lighter than 40 lb children).

An example of a heavy rotor.

This was obviously not a conspiracy to torture female lab members, but a form of tough love (I'm pretty sure this female PI was sane). She knew that it took a lot of toughness to get to her position -- I'm sure it was difficult back in the day to rise up the academic ladder as a woman -- and she didn't want her students or post-docs to allow the lab culture to return to the days of yore. I would have thought that she wanted her lab to represent the step forward made by the women of her era in the world of research and science, even if it were in the details.

So this is what Qinghong told me. I told him (three years ago) that I understood, but the carboy was still really heavy, and I don't think there was any way to bring it down, but that I would try. I went over to the carboy, had one foot on the step stool and one foot on the sink counter when the pGU ran over to me (I think? or some other folks in the lab) helped me bring it down. I probably would've killed my back otherwise.

Nevertheless, I did remember Qinghong's lesson, despite not being able to live up to it. It can be very, very tempting to ask a nearby, stronger male to help you do a tough, physical, but otherwise minor task in the lab, and it always starts out with the impossible/difficult tasks for which you ask their help. And then slowly, you become more dependent on them for the tasks for the medium tasks.

Or the tasks that you might be able to do, but aren't sure. So you ask someone to do it for you.

Or the tasks that you just don't feel like doing.

You get the idea.

I mean, not always, but it certainly CAN be!

I can, at least, attest to this. I normally like to feel self-sufficient, but I'm inherently lazy (it's part of human nature) and sometimes in the kitchen, I ask for consultation from the pGU and I realize my life is a little easier. Recently, I had been noticing that I would ask the pGU for more and more help, just because he was around and could come, and sometimes just because I didn't want to do things that I could have easily done myself.

In the end, I think self-sufficiency is optimal (though when you really DO need help and consultation, ask!), so for those heavy carboys and centrifuge rotors, I may just have to go to the gym after all.

Urr, well not quite like that.

I'm just gonna put this out there

2011-08-15T22:24:00.004-04:00

I am not going to change my last name when I marry. I get this violent, visceral reaction on Facebook when I see someone's name change (and I don't immediately recognize them) and I still don't understand why women want to change their names.

It seems so strange to me. I mean, a name is something that can be viewed as just a form of an identification (for instance, we could just be called by our social security numbers, or like the names in Ayn Rand's Anthem), but our names are almost core to our identity and often almost are our identity. Why should I change that part of me, just because I have decided to pursue a serious relationship for at least part of my life? And why should that part of me change simply because I have children? I don't mean to debase children (I will definitely have a kid or two, one day!), but I personally don't view that as a turning point in my life to change 33%-50% of my name.

It seems somewhat common in science for women not to change their names (thank goodness, otherwise I would've had a heart attack already...) and I've seen some interesting scenarios where:

1) Husband and wife decide to have a portmanteau of their names (like Engleward as their common surname, as one was Dr. Edward and the other was Dr. Englemann), and that seemed interesting and reasonable to me, though a bit too hippie.

2) Hyphenated last names for both individuals (I saw an "Alt-Lopez" recently -- I am fine with that). It gets unwieldy sometimes, though.

3) The husband taking the wife's name (which is amusing and somewhat counter-cultural, but somehow I feel uncomfortable about that.)

Taking the husband's name still represents submissiveness/the existence of a dominating party to me. One post-doc was very upset to hear someone (not me, actually!) object to the idea of the wife taking the husband's name.

Why does it seem that Christian wives almost always (I can't offer a percentage, but I don't see very many exceptions) take the husband's name? What's the reasoning behind this, because the children will have the father's last name? (I'm fine with children taking the father's name, just because hyperhyphenation gets crazy and you need to keep track of genealogy in some reliable way.) But what about "For this reason a man will leave his father and mother and be united to his wife, and they will become one flesh" (Genesis 2:24)? I could almost vouch for Choice #1 through biblical literalism and amalgamation of the two surnames.

Oh, and I'm often appalled when someone asks if I'm going to be "Grace M_____" when I get married. (I have gotten this a lot.)

The answer? NO WAY.

I am my father's daughter, and for lineage purposes, I have this surname. I am proud of this surname because I am proud to be of this family. I have been Grace Yuen for 20-something odd years and I WILL CONTINUE TO BE GRACE J. YUEN FOR THE NEXT 80+ YEARS. Because I am myself . End of discussion.

I guess I'm just not very traditional. ^___^;;

...but anyway, I respect what people choose for themselves. There is obviously a huge cultural reason for why people do the things they do and I respect people no matter what they choose for themselves. I'm just ranting because I've probably seen 8+ young women my age change their names and I don't see why they chose to.

I will never make it big in India

2011-08-15T21:47:00.002-04:00

After my fake-attempt to become a Maggi celebrity, I remember the pGU was making parathas (the nearly ready-made food he eats, aside from Indian pickle and yogurt) on the pan.

I told the pGU, "Hey, who's that woman? I can be on the front of Ashoka frozen parathas too!"

The pGU corrected me. "She won Miss India. That would be Juhi Chawla."

Oh well, there goes that dream. I don't think I could win Miss India.

Somehow there is this multiplicative effect of the scariness of the two pictures. Oops.

Oh well, maybe one day.

Things I think about while at the microscope

2011-08-15T20:00:00.000-04:00

I don't know why, but sometimes while I am at the dissecting microscope, picking a bunch of worms off a plate, I think about the strangest things. I suppose the exercise is often so mind-numbing, it is not surprising what the brain floats off to ponder about. I wonder if I will be doomed for the D.C. marathon, when I will be left alone to my thoughts for 4-5 hours.

One thing that I thought about was a situation I was in recently. I had a life-changing moment after something rather banal. Actually, it was EXTREMELY banal. I do think that most of my life-changing moments (I suppose I have had one or two major ones, can I even use the word "most"?) come from such banal experiences.

Anyway, so recently, I lost my brass rat ring, or at least, I was pretty sure I lost it because I looked for it for a full month, calling the MIT Campus Police, the DAPER Athletics Center -- I mean, I really called everyone I could and.there was no luck. Finally, I gave up and called the company that makes our brass rats, Balfour. I told the representative my story and that I wanted to know how much it would cost. She asked me to sit down to hear the price of my celestrium brass rat. I thought this was unnecessary until I heard the figure: it would be $380.

Can you imagine that? It was already pathetic that I paid $60-80 for a piece of glorified stainless steel, but now they wanted me to pay 5-6x that amount? It was a freaking highway robbery! And so, instead of giving up and shelling out the money, I thought I would just keep searching around MIT and finding more groundskeepers to talk.

And so I searched for weeks...and then a month. No luck.

I contacted the Balfour representative and sent her this sob-story email (which was sincere, because that's how depressed I was). You can skip the emails, which I've put in small print, if it's too boring.

~~~~~~~~~~~~~~~~~~~~~~~~~~

Dear Peg,

I'm Timocita [except I used my real name], an MIT alum who graduated in 2009. We spoke a couple weeks ago, after my celestrium brass rat had been stolen, and left a message recently on your voicemail.

I had a question about the ring loss protection plan. I made my purchase in February 2007 for both the gold and celestrium brass rats and received them late April (a few days after the Ring Delivery event). I find it strange that the ring loss protection plan is only in effect for four years from the date of purchase on all original Rings, since the ring could not possibly be lost between the purchase date and the date I received my ring -- a span off 60 days. If instead, the ring loss protection plan were in effect from the date of ring delivery, then my lost brass rat would still be eligible for a single replacement, under the four year warranty.

My ring was stolen, along with my watch, while I was practicing Tae Kwon Do at MIT on April 21. Between then and the time we spoke, I had been making frequent calls to the MIT Lost and Found, Athletic Center, Police and shuttle services, but waited until there really was no sign of my ring to finally call you. As a graduate student with college loans still to pay, a little savings would mean a lot to me, and certainly go a very long way. I can scrape by to pay $100 for a replacement brass rat, as my budget has become very tight. I know everyone seems to be in this boat, especially with the economy these days, but I am just very proud of being from MIT, but $380 would be very hard on me.

I understand that Balfour must be very busy this time of year, and to make an extra MIT brassrat would halt productivity. If this is a problem, I do not mind waiting until production is less hectic to receive a replacement ring.

If I have no other option than to buy a new ring, I would also like to know what the warranty is on the new celestrium ring. Also, how much would a new gold ring cost? Can Balfour also buy back my original gold ring?

Thank you very much for your time and help.

Sincerely,
Timocita [obviously not my real name]

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

She replied, just following the rules (heartless Balfour fiends):

Hi Timocita

I am sorry but it is not possible to change the terms of the policy. It is an insurance policy and there is no wiggle room. I apologize for not being able to accommodate your request.

The new ring would come with a 4 year replacement policy from the time you order the ring. You can trade in your gold ring if you like and we can charge just a remake fee of $85 plus $14.95 shipping and handling and sales tax or you can get the gold trade-in value for the ring. It would depend on the metal. 10K is $70, 14K is $100 and 18K is $135.

Costs of the new ring are attached.

You might also be able to file a claim under your own insurance for the replacement cost of the ring.

Please let me know if you have any further questions. Thank you for your consideration.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Terrible. And so, I waited...10 days.

Yeah, I know it was pathetic, but sometimes when you try so hard looking for something you've lost (I posted on Craigslist, called MIT Campus Police, DAPER, Buildings and Grounds...daily!), you start to give up.

It was at this time that I had an epiphany though. What was the epiphany?

I realized I was poor.

You know, it wasn't that I was really poor -- not like I lived in a cardboard box, didn't have food to eat and didn't have clothes. I OBVIOUSLY don't mean that! (Just like when a certain pastor reprimands us for saying we are hungry and forces us to compare our hunger for starving children -- we obviously don't know true hunger, but it still IS HUNGER, fool!)

I was too poor to replace something I lost. Moreover, I was being robbed by the Balfour fiends, who were going to charge me $380 for a piece of stainless steel that took them NO MORE EFFORT to make four years post my receiving the LAST ring, and who said that if I traded in my GOLD ring, I would still have to pay $100 to "remake" my freaking stainless steel ring.

You know what that is?
That's right, folks. This was my life-changing experience of the year (maybe this happens ever four or five years) where I learned that:

(1) I was poor. And I actually needed and wanted money.

And sadly, from then on, I began to crave money and saving money. It didn't just feel good when I saved money with coupons or depositing money in the bank. I felt like some justice was being done and I would go wild. I started signing up for random psychology tests, AJE (which is Grade A Bull also, and I will rant about it some other time), you name it. If they gave me money, I had money to spare. I became very hungry for money.

(2) I realized that there are some bad scams in the world, like Balfour.

Let's allow the Course 7 grad to do a back of the envelope calculation. If I traded in my gold ring because I was *desperate* to get my celestrium ring, how BAD of an idea would this be?

It is hard finding out the weight of my gold ring, but let's pretend it is 1.5-times the weight of my celestrium ring (9.1 g, I just weighed it in lab). That makes my ring about 14 grams. The value of that much 14K gold is $463!!!!! In this economy, anyone in their right mind should just keep their gold -- the brass rat may be worth more than our savings after a QE5 or QE6.

(3) Balfour didn't even try to listen to my reasoning on why it makes no sense to have a ring loss policy in effect during a time when I didn't even have possession of the ring.

(4) If someone really did take my ring, that would absolutely suck. It's stainless steel for him (so if he goes to the pawn shop, he gets absolutely nothing), whereas it is a huge loss for me because it (a) has meaning for me and (b) costs $380 to replace. Were there really such people who wouldn't return it? I had much more faith in the world than that. :(

(5) Did I not mention that the damn ring is worthless to begin with????

In the end, I decided that I would shell out the money, which is when I really felt depressed. My justification was that I was so miserable without the ring that I really did need a replacement, and because life is short, I should just spend the money and be done with it. The pGU even said that one day, I would make enough money to not have to worry about this fecality. (Fecality = sh_t in thymocyte terms.)

And the best thing happened. As I was about to ask the Balfour rep where to send the $380 check, the pGU decides he wants to clean out his fish tank water. I hate doing that, so I told him I didn't want to. He did and as he was taking out these large buckets from under the desk for filling up with water, he realized there was something in it.

"What's this?" he said, pulling out a black Casio calculator watch.

He stuck his hand in the bucket again -- he pulled out my brass rat.

You can imagine what my reaction was -- just utter elation. For one, I was glad that my faith in the world was restored (no one actually took it! I was just stupid and it dropped inside the bucket long time back and I never would have known!). I was screaming with joy and when I was done doing that, the pGU helped me write an email to the Balfour rep, which ended with this:

"Life is strange."

It is indeed. At least for me, since even these small events turn into big ones. Like how losing a brass rat and finding it again is the pivotal event in my life that makes me realize that I need to make more money so I won't have these sort of problems in the future, and not just for brass rats.

...oh yes, and Balfour advice.

MIT kiddies, buy a gold brass rat (pick a higher karat, I think), and then "lose" it. Well, tell Balfour that. You'll only have to pay $100 for the new one and you'll be making quite a bit of money as a result. In fact, I advocate that everyone should do this with the gold brass rat. Even if you don't run Balfour out of business, they certainly will be a bit peeved with their company's loss.

They can afford to take a hit to their pocket; you can't.

Soul-searching (no, not the cheesy kind)

2011-08-15T14:14:00.007-04:00

It's funny sometimes when you think about how you go through phases -- there are certainly good kinds and not-as-good times. ("Hey, remember my narcotics phase? Harharhar!") No, that's not what I'm talking about.

My music listening would go through huge phases, at least before the days of Pandora, Grooveshark and Spotify. When I was in middle/high school, my dad gave me an mp3/cd/radio walkman that I loved (though I think I eventually gave it to my vision-impaired cousin, who loved it too -- he really enjoys music, as you can imagine). From the radio, I finally got to listen to pop music (which my parents abhorred and barred me from listening to) and I found out that it was SO DARN CATCHY! ...and then I realized that after a week listening to those songs, they were just painful earworms.

I also went through a Cantonese Opera phase (yay for Kazaa! I miss it), an American folk phase (Joan Baez and Bob Dylan -- I still like folksy/borderline-country music a lot), and an indie rock phase (do Weezer, Phantom Planet, Rooney and Kula Shaker count? no, I guess they're a bit diverse...but you get the idea.)
What I really mean to mention is the fact that I also go through phases of things that I get obsessed about -- as in, things that I think about obsessively, things that I read obsessively, and so forth. This blog, in fact, started out from a fundamental, introspective question that I could not resolve, which was this:

"How do I reconcile my faith in the light of biology?"

It was a painful question that required much soul-searching in the sense that it was energy-draining and time-consuming, leading to my subscription to probably 40+ blogs on the topic of God and evolution. (The only answer I was able to accept was, sadly, simple. I will describe that process some other time.)

No, I didn't "doctor" this. Isn't it unnerving?

Nowadays, I don't really have something that I think about obsessively. I used to read tons of blogs (after that soul-searching point) about biology and got somewhat into the world of popularizing science for the average layperson. That wasn't so fulfilling in the end and was only a short-lived obsession, mainly because I was pessimist about its effectiveness and goals. I also don't feel super-strongly about the popular science and education programs that many of the Harvard students are into.

While many students in my program are interested in Science In The News (SITN, a great group involved in popularizing science and Cambridge Science Festival-type activities), I didn't feel extremely passionate about it. Some people define or identify their passions by examining what they do in their spare time. I've had some spare time recently, but my extracurriculars are namely (1) Tae Kwon Do (which I practice, but I don't consider myself a real TKD person), and (2) TeamAIDAsha (running a marathon for charity, and I don't consider myself a running person or an activist type, at least for something that is a bit harder for me to appreciate).

I long to find another similar, obsessive passion that drives me, and I don't think there has to be some sort of life-changing event for me to again reveal that obsessive passion. I suppose that recently, I have been doing this cooking/baking stuff, but I certainly don't consider that a passion. It's much more related to survival -- the last time I didn't look at a tried-and-true recipe, I ended up making some horrible mushroom soup that was very, very bitter. (I don't even know why, but probably putting a jasmine tea bag in the soup didn't help. Don't ask.)

The pGU used to rave about the evolution-creationism "debates," but has now moved onto reading about the economy (e.g. Ron Paul, Social Security, Obamacare, etc.) When I see him very excited about these issues and energetically debating about them, I almost feel a bit jealous and sad thinking that I don't have a corresponding topic that I feel as strongly about.

(I did have a somewhat life-changing, odd experience that made me realize I was poor, though...but that is for another post.)

Maybe it will take a life-altering, tidal wave event to help me find my next intellectual obsession.

...then again, I do like writing about my experiences, my family and life in general. :)

Last weekend's cooking frenzy

2011-08-10T13:54:00.010-04:00

I never used to bake because I always associated it with those awful girly/matronly things, like knitting, stitching, etc., and certainly never wanted to be associated with anything of that sort. I'm that sort of person who loathes wearing dresses (I often go underdressed to parties, but I don't always realize it....), looking pretty (read: presentable), shopping (when my mom would take me to the store, I would moan and groan, "My brain is dying!" and beg my mom to finish her shopping soon.

Well, Twilight brain damage is more severe.

No, that incident didn't happen when I was five. It happened probably a year or so ago. ^___^;;

Anyway, the point is that these days, I actually have been baking! To keep me (and the pGU) from getting fat from all these sugary and buttery delights, I usually pass them onto the lab as fast as I can. I also convinced myself that it's okay to bake once in a while because following a recipe is just like following a protocol! I mean, as long as the protocol isn't flawed, you should be good to go, right?

(Yeah, it really did take me a long time to not feel ashamed for endeavoring in such feminine pursuits as baking.)

Dr. Chu (my mentor from North Shore, where I did my first real research starting in high school!) was the one who used to tell me that doing experiments is just like cooking. He asked, "Do you cook?" No, I never did.

Well, now I do, but I realized that protocols are more like baking. I feel like cooking isn't nearly as straightforward. Baking is like setting up a PCR reaction and running it on a gel. Cooking is more like some gigantic and daunting cloning project from start to finish. The connection really is there, though! (I'll probably edit this once I get creative ideas from you guys.)

Well, you get the general idea. Most things that I've baked came out fine -- banana bread (vegan and regular), ginger molasses cookies, coffee + walnut cake, for instance. I repeatedly baked a flan that I fed to people, who eventually let me in on the fact that it didn't taste like flans that you could buy outside (I blame the recipe for that!).

Last weekend, I consigned the pGU to help me make Sesame Seed Balls (煎堆 or 麻团) and Almond Cookies. It took six hours and killed the motors of two blenders (as in, they no longer work).

Well, that's what they're supposed to look like.

In the end, I made a critical substitution of oil and butter in place of lard (yes, they go into these cookies) and that made the cookies very crumbly. Also, the stupid recipe called for almond extract, which was later not nearly enough.

The sesame seed balls were the real nightmare. Glutinous rice flour is extremely sticky and when it's that sticky, it doesn't roll into a ball. It was hard enough just mixing it -- the first blender we used got fried, so we went to Target to buy a hand-held electric mixer, which also broke. It was just disastrous and the deep-frying (yeah, they're unhealthy) took forever, especially for the 30 sesame seed balls we had. And with so many fried sesame balls, it was hard to figure out what to do with them, so the best option was to bring them to lab and let the lab vultures eat them (which worked very well!).

In the end, I will probably not bake unless I need to. I don't have unlimited time and I think baking is only good for me when I'm absolutely bored and have nothing better to do (maybe this is why people bake, period?) or if I need to take my mind off something (when I'm so stressed that I can't function, I bake, it seems...)

Til then, I will just cook my lunches and dinners. ^____^;;

Welcoming myself back to Blogger

2011-08-05T01:29:00.001-04:00

I sort of feel bad that I haven't been blogging for a while. Somehow, I just became extremely busy and a bit stressed about lab work, which led me to my plummeting into long, taxing experiments that often didn't even work (or if they did, they weren't very informative).

Lots of things have also been happening in my life. I wouldn't say that they're really milestones, mainly because that would make my life seem rather drab and pathetic, but they are sort of important at least. This summer was the first time I (1) consistently cooked for myself and brought my own lunches, (2) moved out of the dormitory for good to find my own place, (3) signed up to run a marathon, and (4) presented my own data at my own lab meeting. In the dull life of the Timocita, this is pretty substantial.

I've also been leaning more and more towards vegetarianism, which is often very challenging. As my parents completely disapprove of the idea, they refuse to help me find out authentic Cantonese vegetarian dishes. Maybe there just aren't any? (uh...)

I've also felt that my life has become so drab (day-in and day-out is lab), what could I possibly say that is worth ANYONE reading it? I used to write white a bit about religion and science, but I've sort of settled that out for myself, and when I feel comfortable, maybe I will share it with the rest of the world.

...but what do I write about now? I guess maybe I'll try to jot things down that amaze me. I don't have much insight into any real issue of importance (economics, healthcare, etc.), but I am easily amused at random things in life.

I suppose I will just write about those.

A cool talk about black holes in Cambridge -- today!

2011-05-04T11:43:00.003-04:00

Harvard's Science in the News (SITN) is a student group of PhD students at Harvard University, whose mission is to examine the science behind the media reports we hear everyday, to delve a little deeper into the science and bring that information to you so you might better distinguish scientific fact from pure speculation.

Today, May 4th, SITN will be kicking off its first-ever Spring Lecture series in Cambridge, MA! The lectures will be held from 7-9PM at Pfizer Auditorium at the Cambridge Campus of Harvard University.

Today's talk will be on the elusive Black Holes --everyone's heard of them, but what are they? The talk will be a great kickoff to the new Cambridge series, so come! Here's the line-up for the rest of the spring:

May 4	Black Holes and Cosmic Roles: Understanding the Center of the Galaxy
May 18	The Mystery of Sleep: How Neuroscientists are Solving One of the Brains Most Interesting Puzzles
June 1	Origins and Applications of Pluripotent Stem Cells
June 15	The War on Cancer: Where we Are in the Battle, and Why we Haven’t Won.

These talks will be held from 7PM – 9PM in the Pfizer Auditorium Hall at Harvard University (Mallinckrodt Building, 12 Oxford St, Cambridge).

See you there!

Why my PI is awesome, Reason #3472

2011-03-23T19:58:00.001-04:00

Reason #3472:

At the end of my practice PQE talk, he asked me "This will sound stupid, but what are you planning to wear for the exam?" to make sure that I would dress comfortably, since I would be stressed and the exam would take two hours.

:) Big happy face.

Since my PQE has been rescheduled...

2011-03-02T15:08:00.001-05:00

...not only do I get a few extra weeks, but I have a new countdown clock ready!

Countdown to my PQE: 29 days!?!

2011-02-06T20:01:00.006-05:00

HOLY CRAPPAGE.

As you know, I have my preliminary qualifying exam (PQE) in 29 days, on March 8, 2011. It's the same day as international Women's Day, the "only day in Russia in which women are not beaten," joked a Russian post-doc in my lab.

Talking to my professor about my specific aims has certainly de-stressed me, particularly because the conversation helped me re-shape my thoughts on how to outline my experiments.

I've also just realized how hard it can be to balance experiments and proposal writing, and I think this is particular tough when you are on a project that is just budding, and there are so many open questions. Additionally, my project allows me to test simple hypotheses extremely quickly (with the instant gratification of assays being something as quick as...biochemistry). It doesn't get any better than that.

That said, I ended up staggering my experiments, but not separating them -- to the point (and my detriment) of having a full experiment every day. It would end up looking like this:

Monday: Set up experiment.
Tuesday: Score Monday's experiment, set up another experiment.
Wednesday: Score Monday and Tuesday's experiments, set up another experiment.
Thursday: You are SF-stacked.

This problem is so simple to solve: you just should not do experiments like this. And at the same time, it's so tempting -- you could troubleshoot many conditions in just a week, and the generation time of C. elegans at 20 degrees C is only three days, so it takes so little effort to just do "one more experiment."

That said, I spent most of Saturday just running all around the lab, making bacteria media, picking worms off plates, scoring assays, etc. It was absolutely nuts, and at the end of the day, I couldn't do anything out of exhaustion, least of all, my proposal (probably >>> important than my experiments...)

I think the simplest solution that I need to take is just to stop experiments, as the pGU has suggested -- it's smart, and forces you to focus and not go into lab, because what happens in my mind (at least) is "Oh no, if I just go in and do something small for an hour, that doesn't take much time...." and in actuality, I end up staying there for hours on end, preparing for future experiments.

I also liked the pGU's suggestion of just bringing worm plates back from the lab to my room. "I mean, all you need is a 25 degree C incubator. In your thesis, you don't have to say WHERE the assay was scored. You just have to say that they were kept in an incubator!"

You know, this is true -- unlike people who do real immunology, I don't need a sterile ANYTHING. I just need a space that's moderately clean.

Unfortunately, I would also need a decent microscope in my room.
I wonder if I can use fellowship money to purchase another microscope, and convince my PI to let me do that,. Technically, I don't need an incubator, if my room temperature is close enough! But then again, there would be a higher chance that I'll inoculate myself with a virulent Enterococcus strain. It's bad enough that I don't always use gloves.

>>In other news, I made it to my lab's website -- YAY!

I chose a serious photo to remind people that as giddy, hyper and random as I am, I'm seriously training to be a biologist. ^____^;;;

Why my thesis advisor is the best, Part II

2011-02-04T14:13:00.004-05:00

"[The preliminary qualifying exam] is not an exam. It isn't. We're way past that point.

And you're supposed to be getting past the student-teacher mentality. This is a discussion among peers, and you want their feedback. You should take charge of the discussion, and if they want to ask you questions, they can."

-My advisor's opinion on the PQE.

(I will certainly try to do that. ^___^)

C. elegans papers can be fun

2011-02-01T13:12:00.003-05:00

For instance, in a recent paper reporting the discovery of natural viruses infecting wild isolates of C. elegans and its relative C. briggsae.

"JU1264 [a specific C. briggsae isolate, closely related to C. elegans] was isolated from a snail collected on rotting grapes in Santeuil (Val d’Oise, France) on 14 Oct 2007. JU1580 [a C. elegans isolate] was isolated from a rotting apple sampled in Orsay (Essonne, France) on 6 Oct 2008."

Yes, they really did go into the wild and collect virus-infected C. elegans. It's sort of fun if you try to picture it in your mind:

It's a virus on a worm on a snail on rotting grapes in France!

...okay, maybe it was funny in my mind, but probably just because it reminded me of the children's book There Was an Old Lady Who Swallowed a Fly.

Biology Lab Parody of Lady Gaga's "Bad Romance"

2011-01-23T10:46:00.005-05:00

It is unquestionably the best Lady Gaga "Bad Romance" parody ever.

And even better, it's about being a grad student in biology! (Yes, we are jaded, but some of us have an extremely good sense of humor.)

If you know the original, you'll appreciate:

1. The directing
2. The lab-related crazy, Gaga-type dress
3. The fact that when the original Gaga speaks French, this lab Gaga speaks CHINESE!!!

I laughed so hard the first time that I cried. It was beautiful.

Zheng Lab at Baylor College of Medicine, you guys ROCK! You even got the post-docs to dance. ;)

I don't think this works as motivation.

2011-01-14T16:59:00.001-05:00

(Note: PQE, or Preliminary Qualifying Exam, is when grad students propose their intended thesis projects and then are grilled by a panel of three professors, where their background knowledge and scientific-thought-process are evaluated.

In other languages, PQE is frequently translated as "armageddon."

PQE Madness

2010-12-29T21:01:00.005-05:00

I scheduled my preliminary qualifying exam (PQE) for March 8, 2011. It's apparently international Women's Day (celebrating the protection of women?), or as one Russian post-doc in my lab joked, the only day in which women don't get beaten. There's also a Children's Day, if you don't know.

Anyway, the point is that I think I'm effed for it. It's even gotten to my subconscious. I mean, I think I had a dream recently (that I don't quite remember) about Cryptococcus neoformans. It's not as if I saw budding yeast in my dream or anything. The term that keeps popping up in my head is "Cryptococcus neoformans."

I mean, I don't even work on Cryptococcus neoformans -- I'm going to be working on Enterococcus!

I also had some bizarre dream where one of the Wednesday immunology speakers (who I will be having dinner with) was going to be on my PQE committee, along with a whole bunch of people who were NOT my committee members in real life (as in, some of them were my professors from the past). And then, one of the dream committee members told me that this immunology seminar speaker would not be able to serve on my PQE committee. Because he was jailed. ("But don't worry!" the faculty member attempted to reassure me. "He just has some business he needs to take care of.")

!?!?

I think I understand why one grad student said she felt as if she were having a mental breakdown.

I dreamed a dream...

2010-11-12T08:32:00.002-05:00

I usually don't post my dreams here, but you'll see why I wrote about this one:

I had a dream that I had to go to the doctor because I was itching all over. My doctor asked to look at my belly, and there we saw small impressions all over, in the shape of either a small circle within a small square, or a small circle within a circle. They looked as if someone used the end of some pen and pressed it all over -- very odd.

Then I was complaining that my head was itching a lot, and when my doctor looked, there were gigantic C. elegans (like 6-8 inches long or something -- think SLUGS) swarming all over my head, and probably 50-100 of them. It was absolutely horrifying.

(This is a slug, not C. elegans.)

....so I think this is what happens when quals are rolling around the corner. When you've joined a C. elegans lab and are stressed (and have compulsive disorders such as scratching your head, like I do), you end up dreaming about the weirdest things.

Get used to feeling stupid

2010-10-27T11:49:00.004-04:00

One of the more senior immunology grad students (I actually saw her just the other day at a DFCI-BWH seminar) wrote a short advice-type article about the grad school experience in the DMS Bulletin.

What caught my eye was her advice to "Get used to stupidity." She doesn't urge you to get used to other people's stupidity -- that would be rather arrogant -- but to the idea that you are stupid, and maybe everyone is.

She references this very interesting (and yes, a bit disparaging) article written by a professor who did his grad work at Stanford. In it, he talks about how we often feel really stupid during the course of a PhD.

It's an interesting read from the perspective of a professor looking back at his grad school years, and reminds the reader that absolute stupidity (the fact that we really know so little about biology) is what drives research, and while you might think that your PI and other professors must know the answer, they don't -- and that's why it's an important question in the first place.

It's also reaffirms the idea that research is hard (which, I think, is not truly apparent at its greatest level until you actually start doing the research).

Heartwarming stuff, isn't it? ^___________^;;

I AM DONE WITH GRADING!!!!

2010-10-25T17:03:00.003-04:00

Yes, that deserves a post.

Also, I've been meaning to post the Hojutnuis Production of Justin Bieber's "Baby" - The MIT Version.

Singing and video editing by my cousin Danielle, rapping and bad dancing by yours truly.

Okay, time for real life. :)

Yeahyeah, as in real grad school life. ^_______^;;

On the other side of the fence

2010-10-21T14:14:00.003-04:00

It is truly a bizarre experience to be a first-time TA (yes, there's a first time for everything, you can stop now) when you've always been a student.

For instance, all the times when you think your TAs are just lazy and incompetent, it's likely that they aren't. It's just that TAing is hard -- the preparation for it, the scut-type work (photocopying exams, editing things, sending diplomatic emails), and coordinating with students, other TAs and faculty. I always say things are not trivial, but TAing really isn't trivial -- or at least, good TAing.

For instance, to write a good exam question takes much longer than to actually answer the given exam question. You would think that writing exam questions is fun (in a way, it definitely is! I had fun, at least), but it's tough: the wording must be appropriate and clear, the prompt to the question must be lucid, the figures have to be concise and decipherable, and you still may throw the student off due to oversight.

Your interpretation of a question as a TA is skewed because you knew beforehand what you wanted to ask -- you were just thinking about how to ask it in such a way that it could be answered. Your poor student who is trying to make his way through the 19 page exam is just barely trying to comprehend enough of the given information as to maximize the number of points per second spent on the question.

That said, I'm sitting in the exam room where about 35 students are racking their brains to answer hard questions that are worth a couple of points. It's weird sitting in front of them, watching them fidget, scratch their head, erase answers, bite their fingernails (I do that when I'm nervous), and struggle.

So my friend MHC, when she hears about my TAing experience (for her program, they don't have to TA), and asks, "Oooh! How does it feel to be on the other side of the fence?"

I don't know, it's just a very strange feeling for me -- partially because I'm younger than all my students (they made this clear to me when I told them I refer to them as my "kids"), and also because I don't feel like I know any more information than they do. In fact, I think my students are much sharper and brighter than I am.

Anyway, I'll see if I can post about the grades. I should write more on this blog. Poor blog, it has been neglected for a while.

In more exciting news, tomorrow is the Harvard Immunology 2010 "RETREAT"! Kumari designed a *fabulous* (I feel rather gay when I say *FABULOUS,* but not lesbian) shirt. I will ask her if I can post it here. :)

Why my PI is the best PI in the world

2010-10-21T14:02:00.003-04:00

It should probably be a running list, but watch me delete this post in three years after I've become a calloused, bitter grad student. (Just kidding!)

Today, I was very late in photocopying exams for the Imm201 class (multi-factorial reasons) and everything that could go wrong went wrong.

....as in, I printed 10 copies of the wrong version of the exam.

....and then the copies I printed weren't collated. (Or stapled.)

....and I still needed to get to Longwood from MGH and had missed the Partners Shuttle.

My PI saw me struggling and looking really frazzled, so not only did he give me $20 for cab fare to get to Longwood in 10 minutes, but he also helped staple and collate 10 of the exams. (The new post-doc and I worked on the other 10.)

I think people pick their thesis labs for many different reasons, and for some, it can be a hard decision. Yesterday, a post-doc from my first rotation lab was talking about how the PIs of the first rotation lab were being very nurturing to the graduate students, and this made me a bit wistful. I really loved that lab, loved the people, and the PI, and the general direction of the lab, and yet I chose another lab in which to do my thesis -- for a series of complex reasons.

But I think today I am truly glad about my decision, and while I can always daydream about what it would have been like to join my first rotation lab, I think I chose my thesis lab for the right reasons, and that it was a good choice.

The Cantabrigian Lifestyle

2010-10-18T19:47:00.003-04:00

I think I'm finally living it up (sort of - as much as a graduate student can without funds). I'm having 铁观音 (tiě guānyīn) tea with Kumari (of Team Harriet and Kumari fame), in Dado Tea, doing TA-related work. Meanwhile, the cafe (thefé?) is playing Indian-Reggae-ified music.

I'm certainly enjoying this part of my life in Cambridge. :)

Man, I need to start posting again.

2010-10-12T10:07:00.004-04:00

I think it's a shame that I haven't written anything here since my France trip. It's actually mind-boggling.

So, I think I'll start writing again when I have the time (or when I need to de-stress). This week started out rough and will only get rougher (Friday is the genetics midterm, whose material I am truly unprepared for.)

The good thing is, I presented a paper on a RIG-I-like gene involved in antiviral siRNA silencing and the journal club seems to have gone fine.

DUMPY WORMS! :)

...okay, more to come later.

[Rather unfair] Observations about France

2010-06-14T12:10:00.008-04:00

The disclaimer is just so that I avoid hate mail. But hey, I should be able to put whatever I want on my blog, right? For the record, I really am enjoying my stay in France, but there still is a bit of cultural shock I'm dealing with, so bear with me.

I've been in Marseille-Luminy for about two weeks and change, but haven't been able to update much. This is partially because I've been pretty busy (why do I always pick the intense labs for my rotations?) but also because I've had some trouble thinking about things to write about.

And so, on my caffeine high, I will write down a few points.

1. France is good about conserving water.

The best example is that toilets have "dual-flush" options. Now, what do I mean by that?

Behold -- the dual-flush button. This is actually an awesome idea. You press the smaller button (right half) for minor tasks and the larger button (left half) for heavy-duty tasks. I mean, why should you have to waste water -- the most precious commodity on Earth?

2. The French are not as good about recycling.

That said, there is little recycling done here -- I'm not even talking about the lack of single-stream recycling. I just don't see recycling, period. Papers and plastics still have the "recycle" sign on them, but there's no bin for them. And so, everything (nearly) goes to the trash, or a very limited variety of waste is recycled.

It seems as if there is a disconnect between the ideology behind saving water and recycling, unless it's an issue of cost?

3. Bathrooms don't seem to be as well ventilated.

This is at least true where I'm working, as the bathrooms smell a little "out-housey." It just seems as if there's no need for a crazy amount of ventilation. I'm not really sure what the issue is.

4. People know how to live.

I don't mean this in a condescending way -- it seems that life is just as productive as in the U.S., but that people take their time. "Fast food" is an abomination because lunch is sacred (more sacred than Sundays, it seems) and people take their time for lunch. It's an hour, at least....and after lunch, there are coffee breaks. "Taking a coffee" is not frowned upon, if you can spare the time, and I think that's great.

Until you turn into this particular Frenchman:

I really sympathize with this guy. Caffeine can really make you do crazy things.

5. Dog poo is rampant on the streets of France.

I can't tell you how many times I nearly stepped in dog poop. It's absolutely disgusting -- while Marseille had about as much as NYC (I encountered tons of it on my way to Rockefeller University when I was working there), Arles is sooooo much worse. Even in the U.S., I would advocate for some law that allowed vigilantes to go around (with gloves), pick up dog poop, and mash it into the face of a dog owner who did not curb his dog. (It's obviously not the dog's fault, so the dog should go unharmed.)

6. Europeans really do seem to enjoy techno music.

Or as poor Kim from my program found out, they like remixes, and will remix anything. Acoustic music, mellow rock, you name it. It can be remixed and you can dance to anything.

7. There is a lot of American music played in France.

I'm not even sure why, especially since French music is really good. While I can hear Lady Gaga everywhere I go, the lab (and post office) seem to enjoy listening to super retro music. I heard "Total Eclipse of the Heart" in the post office one day and was really surprised.

They're also really into American media (since the Americans don't produce anything

8. Sometimes I think that the French are the Japanese of Europe.

Now, don't take this the wrong way, because I know people will freak out about me saying this. (This is not meant in the way that it has been said that "the Chinese are the Jews of Asia".) I just meant that the French have a very good appreciation for (1) presentation of food, (2) delicacy in general, (3) courtesy, etiquette and the importance of greetings.

In the same way that if you use the wrong form of a word in Japanese to address someone to say "hello" and can offend them badly, you can also present yourself as extremely rude by using the wrong form of hello to a more conservative shopkeeper (you cannot say "Salut!" and must say "Bonjour" instead. Oh yes, you must say 'hello' as well as 'thank you, goodbye' to a shopkeeper here. It is rude not too.)

Okay, everyone's still offended. Oops?

9. The French do not wave to greet people.

I don't even mean to say that they don't wave frantically like I do, but they just don't wave. You say "Bonjour" and a few other words, but no waving. My waving has amused quite a few people in the lab. Even more interestingly, many Americans think then French are rude, but they really are not.

In Sarah's (my roommate in Marseille) travel guide, it says something to the effect of, "In France, saying hello to strangers is a sign of dementia, not of friendliness (honestly). So don't think the French are rude. It's just part of their culture to have an emphasis on longer-lasting friendships and to devote time to those, not just on fleeting, superficial relationships."

Dude, that was harsh. ^___^;; Granted no one should label a whole culture for being "rude," but there was certainly a better way of saying that. Yeesh.

10. People are very nice here.

It's been said that people in the south of France are very nice. I think that's definitely true (maybe in the same way that people are more "down-to-earth" in the midwest and south of the U.S., possibly because they haven't been absorbed into the fast moving urban world of ambition, distrust and hording.

Sarah and I arrived at an (apparently) one-room bed-and-breakfast place at 7PM, and while the owner had no room, he made at least eight calls to friends who had rooms to find us a place. He then cooked us a multi-course meal that was absolutely delicious (he and his partner/friend are chefs). We were extremely grateful for his kindness and generosity.

11. It is a fact that most European men have smoother cheeks than I do.

Granted, I probably need to shave more (you know, those really hairy Chinese genes), but gosh. I think people use moisturizer a lot or something, because my cheeks and palms are like sandpaper in comparison.

Someone remarked "And how did you come to know about European men's cheeks? Huh??" Obviously by kissing.

No, not that way. People here like to kiss each other on the cheek to greet each other, which must be a cultural shock to many Asian cultures (we don't touch people, ever). You're supposed to start with your left cheek and then make this kissing sound, then go to the right cheek. Some people even do it three times. Granted, people do this in the U.S. too, but I've really never liked this (I still find it odd, after having to kiss 20+ people this way at a house party in Marseille on Friday night), and even then, I've tried to avoid it at all costs.

Yes, I'm one of those people who will awkwardly try to shake people's hands when they're gesturing for a hug or cheek-kiss-thing. I am an insensitive, selfish human being. (Awww, how cute.)

Anyway, more to come. I'm in the process of uploading pictures to Picasa, but you can see what I've put there by clicking the link.

Au 'voir! ^____^;;

I'm in Marseille!

2010-06-05T07:09:00.002-04:00

And my roommate has suggested that learn French this way:

http://yoyo.its.monash.edu.au/~mongoose/french/phrases.html#mangerai

My favorite part was entitled "Do you have anything to declare?"

Hilarious.

What is sticky and brown, and is more epic than an epic fail?

2010-05-29T21:44:00.003-04:00

Nope, it's worse that fecal matter.

It's this.

Folks, we have a new standard for failure.

The Anglerfish's Tale

2010-05-25T17:46:00.006-04:00

Darwin expressed his doubt in the existence of God when he pointed to the example in nature of parasitic wasps, saying:

"I cannot persuade myself that a beneficent and omnipotent God would have designedly created parasitic wasps with the express intention of their feeding within the living bodies of Caterpillars."

You couldn't blame the man once you heard the story about these parasitic wasps.

Here's a picture of a chubby little caterpillar. He's Manduca sexta, or the tobacco hornworm.

What happens is that an adult female wasp will lay her eggs in or on the body of a host insect, say a chubby little caterpillar (specifically, tobacco hornworm). As a result of this parasitism, the caterpillar's behavior will be changed -- the wasp suppresses the caterpillar's feeding by inducing an increase in octopamine in its hemolymph (like blood). This disrupts the motor pattern by the frontal ganglion, preventing the ingestion of food, and essentially making the caterpillar a paralyzed zombie (yes, think about it--). Some wasps are even more frightening: they can alter the escape behavior of its host, perturbing the host's serotonergic system.

Either way, it's bad news for our poor chubby caterpillar. With these neuromodulators, the caterpillar is alive, but paralyzed. This allows its flesh to be used for the growth of young larvae, whose hatchings will eventually kill the host. After all, they're feeding in or on the host, so our friendly caterpillar is a goner. And(!), a single egg laid in the caterpillar can produce multiple offspring.

As terrible a thought as this must have been for Darwin, I think there are even more crazy things in nature that I wish he could have seen.

With that, I give you The Parable of the Anglerfish.

In some ways, I think it's even more disturbing than the bit about the parasitic wasp -- just because it's so bizarre and twisted.

Anyway, this is a public service announcement to say:
If it's that twisted, it just may be evolution.

Brought to you by the makers of:

(Duuuude, I still can't believe it's real.)

I totally missed Everyone Draw Mohammed Day!

2010-05-23T18:12:00.004-04:00

In case you didn't know, last Thursday (May 20) was "Everyone Draw Mohammed Day." It was organized by these folks with the initial purpose of showing extremist Muslims that freedom of speech still exists in some parts of the world, and that if people want to draw harmless pictures of Mohammed, they can.

Unfortunately, this led to a lot of hatred on both sides -- while Pakistan shut down Facebook, people in the U.S. started drawing lots of offensive pictures of Mohammed with pigs, Mohammed as a pig, Mohammed with his 9 year-old child-bride Aisha (as disgusting as that is in today's standards, it was not uncommon -- here's another, but more recent, example). It also is offensive to moderate muslims, whose religious sensibilities (pGU's term) have been offended and deemed collateral damage.

Even so, I saw a woman in a niqab in Boston and felt sad for days, just thinking about it. So, too bad!-- I'm drawing my Mohammed whether you like it or not.

As I like pigs a lot, I would not want them to be associated with my drawing of Mohammed. Therefore, I chose a much more popular animal (at least, in Asia.)

Well, I can't really draw, especially on MS Paint, but you get the drift.

I still like Pharyngula's picture best.

I haven't blogged in ages!

2010-05-12T09:54:00.006-04:00

So I guess I'll come up with 10 random things to say now and then start updating more regularly. (It's been a busy second-half of the semester.)

1. Science in the News (SITN) is a student organization devoted to making science reach the public. I'm peripherally involved in the group, but intend to participate more next year, since I won't be taking classes in my second year.

I wrote a short piece about our commensal bacteria for the SITN flash earlier this month and it got put online, though!

2. I was out of the lab for two days (only two days!) and people asked about my disappearance (in a nice way, though). It's nice to know that people acknowledge my existence.

Or rejoice in my temporary non-existence.

3. I finished my immunology final yesterday. I am done!

4. If Pandora (the internet music service) has an Indian counterpart, I think it should be called Pandoora. It may have issues with intellectual property what-not and this music video.

5. The best instant coffee in the world?

It has roasted chicory in it! Heat some milk, put some Bru and sugar into it, and it beats drip-style coffee any day.

6. That said, if I didn't have Bru, I would probably have an Americano. But only if it were really, really cheap. (Did I mention my first rotation lab had an espresso machine? ^___^)

7. Since I've been (1) the times on Chinese pop music and (2) haven't downloaded music since high school, my ipod has very few songs that I really enjoy listening to. I should go to a library somewhere and borrow CDs.

8. Until then, Pandora has been extremely useful. Since my brain is no longer being used for classes, I try to devote most of my energy to making funny names for my Pandora stations.

You know, like "El Condor Chaurasia" [South American pan flute music + all music related to Hariprasad Chaurasia], "Classical Potpourri" [like "I'll take Classical Potpourri for $200, Alex"], and "All Whales Considered" [songs from NPR's podcast "All Songs Considered" + songs similar to the band Noah and the Whale.]

9. I want to learn Python. It's not only going to prove useful during my PhD, but I think there's something about programming and practicing it that helps you develop a logical method of thinking (writing elegant code is difficult, or as I misspoke to my two PIs from my first rotation lab, "eloquent code."

10. I will be in Marseille, France during the entire month of June! I heard it's very pretty there. The bad thing is that I don't know French at all.

However, I heard that some people can speak some German. I'm wondering if it's worth it to pick up the German (because I had one semester of it?) and then try to talk to people in broken German, or maybe should I just learn French from scratch now.

It's a shame in some sense that I took Latin in middle and high school. ^____^;;

>>Will update on the sake tasting (and aldehyde dehydrogenase deficiency) later!

Devbio-envy: Freudian psychoanalysis for the immunologist

2010-04-14T19:51:00.002-04:00

"Immunologists love this stuff because it makes them think they're developmental biologists." -N. Haining

Sad Picture of the Day

2010-04-13T16:52:00.002-04:00

Now featuring: ob/ob mice.

These mice have a mutation in the leptin gene, which controls appetite. Apparently these mice overeat, becoming obese, and becoming so defensive of their food that they must be housed individually.

According to experimental protocols, ob/ob mice are "sac'd" when they fail the "flop test." This is when the investigator rolls the mouse on its side. If it can't re-position itself to its original state, it will need to be euthanized.

And if you thought the ob/ob mouse was sad, here's the adiponectin-transgenic ob/ob mouse.

"As it turns out overexpressing adiponectin in leptin-deficient mice leads to diminished food intake (relative to body size) and diminished calorie expenditure (lower activity and lower body temperature) relative to leptin-deficiency alone. It also leads to fat accumulation and even more weight gain, resulting in massively obese mice. The balance of energy expenditure and fat accumulation without a change in fat clearance rate suggests enhanced efficiency of fat generation as an important mechanism for obesity in the mice. Despite the weight gain and fat accumulation, the mice were protected from insulin resistance, beta cell failure and diabetes."

Yeah, it's really sad. (And amusing, but still sad.) It's important to keep in mind that though these animals are probably not happy living this way, they were engineered so we could understand the mechanisms of metabolic diseases.

Medical puns and taxonomy

2010-03-02T12:44:00.008-05:00

I had a pretty eventful weekend, which means that now I'm super busy doing work. More posts to come, but I thought I might just share an anecdote or two.

I think you have to know the people involved to understand the subtlety of the humor, though.

1. The pGU's friends from NYC came to Boston with their young daughter (1.5 years old, two?) She likes this plush gorilla and can be very defensive when it is taken away from her.

Rhea, playing with the plush: "Monkey!"
The pGU: "No, Rhea. Ape. Ape."

One day, it's gonna be "No, Rhea. New World Monkey."

2. On physicians.

Thymocyte: "Do you happen to know this professor who is teaching my clinical sessions class? She's...interesting. She thinks that doctors resemble the organs they study."

The pGU: [silence]

Thymocyte: "For instance, she's a dermatologist, and thinks that she's especially strange and unique."

The pGU: "Or superficial."

Thymocyte: "Actually, she said exactly that! She said that contrary to popular belief, they would not be superficial. And then she said rheumatologists would be people who could integrate many different systems in their heads, and are very complex and knowledgeable."
The pGU: "They'd be disjointed."

Thymocyte, laughing: "Okay, that's actually pretty funny. And pathologists?"

The pGU: [pause] "Grave."

Okay, no more bad medical puns for now.

An immunologic-centric view of the world

2010-02-17T16:24:00.001-05:00

And now, a public service announcement:

"Life is the constant reaction to challenge." -Dr. Florian Winau

Happy Piggie Hearts Day!

2010-02-14T14:05:00.004-05:00

My cherished pig calendar from the Bexlites!

Or more formally, Happy Valentine's Day/Single Awareness Day!

A pair of cockatiels from my cousins.

Yayyyyyyyyyyyyy! ^____________^

A caveat on time travel

2010-02-09T13:01:00.006-05:00

No, I mean it.

Today, I got back from staring at my microarray data and checked my email to find this rather bizarre email.

Gmail displayed its title "Real Time Machines (Important if you use)" and I could have sworn it was spam. I didn't quite recognize the email address, but it was labeled as coming from the lab.

This must not be email spam then, right? Why in the world would one of the post-docs be warning us about Time Machines.

WAIT, I thought. Unlessssssssssssssssssss....!!!

....THEY WERE REAL!!!!!

Yes.

Okay, well, as with all things that seem way too good to be true, they usually are. And unfortunately, there was no real time travel for me.

My one second of sheer joy at the idea of actually seeing the Eloi and Mordocks was dashed to pieces.

Real-time PCR.

Ruining the innocent bliss of happy graduate students everywhere.

DAMN YOU, RT-PCR!!!

Maybe one day, la.

FYI for Harvard Immunology interviewees

2010-02-05T10:57:00.003-05:00

In case you feel like you'll have a tough decision between Harvard and Yale:

Yale Shrinks Graduate Programs to Save Money

by Lauren Schenkman

Yale University plans to shrink its incoming class of graduate students by up to 15% as part of an effort to save $50 million in the upcoming academic year. The cost-cutting is a response to a $150-million deficit created by a 29% plunge in its endowment during the recession. Additional steps, announced yesterday by President Richard Levin in a letter to faculty and staff members, include freezing some faculty salaries, "consolidating" services like human resources and information technology, and adjusting thermostats to 68°F in the winter and 75°F in the summer.

Levin said that Yale will boost stipend support by 2% for students in their first few semesters. Research grants pick up the tab after that, explains Steve Girvin, deputy provost for science and technology at Yale and a professor of physics and applied physics.

A Yale graduate department typically enrolls 20 to 30 new students a year. Two or three fewer graduate students per department will mean fewer research assistants from which professors can choose down the line, Girvin says. "It's not the direction that we want to go, but it's necessary in the current financial climate," Girvin says. Witold Skiba, an associate professor of physics and the director of graduate studies for the physics department, worries that "if [the cut] persists for several years, it might start affecting research."

You know what this means, kiddies?

Click the trombone for major sadness.

You sick, sick med students!

2010-02-03T19:22:00.003-05:00

...but I'm really tempted to buy this shirt anyway.

In case you were wondering, though, I do wear crazy shirts on a weekly basis, at least.

Here's the one I was wearing today, which my oldest cousin bought from Thailand.

The PI of my lab even commented on it. Actually, he always comments on the crazy things I wear. This time, his reaction was "I like your shirt!"

Too many crazy shirts to wear, too little time...

Things that make me smile

2010-02-03T09:59:00.003-05:00

My dad will often send me emails (I get at least two "forwards" from him each day). He also subscribes to some site that sends him a quotation each day, and he usually forwards that to me too.

Yesterday's quote that he passed on to me was from Adlai E. Stevenson, who said something HIGHLY reminiscent of a conversation I had with the pGU. My conversation was about how you can tell what a person cares about by what makes him angry.

Adlai Stevenson said, somewhat similarly,
“You can tell the size of a man by the size of the thing that makes him mad.”

I replied to my dad, saying that I appreciated the quote very much. He sent me this amusing reply back [bolding mine]:

This is Adlai Stevenson, not my dad -- in case you were wondering.

"Adlai Stevenson was one of the most intelligent politicians in the US. Unfortunately he was a Democrat. You have to understand that the old Dems especially the ones before Kennedy were quite different from the new Dems. I heard and read about him in Hong Kong. I liked current affairs in addition to my electronics when I was a kid. Stevenson ran against Eisenhower in 1952 and 1956 and lost. One of his famous quote was that when his aide during one election told him that all polls indicated all 'thinking' voters would be voting for him and Stevenson replied, 'Well, but I still need a majority to win'."

Hehehe! I remember that one time when I hadn't called my parents for a while, my dad said, "I can be your [email] penpal!"

Good thing I get to see my parents for Lunar New Year this year! (It falls on President's Day weekend.)

The Harvard Immunology Interview Weekend Talent Show!

2010-02-02T12:16:00.002-05:00

Well, sort of.

I finally got the internet/my computer/YouTube/etc. working and have now posted the videos of Prof. Shiv Pillai's Incantation + Lymphocyte Rap, as well as Sanket and Rohit's tabla performances. Unfortunately I couldn't tape the entire performance, as my camera is old and doesn't take larger SD cards, and I had a total of a little more than 2 GB.

But here they are!

1) "Now you know your G-O-D..."

2) Sanket's third annual tabla performance.

3) Rohit's premiere performance for recruitment!

Enjoy!

(The crazy unofficial Harvard Immunology video will be made...on Thursday night, maybe. I'm swamped for this week...)

The chemistry of chai

2010-02-01T23:23:00.006-05:00

A few days ago, the pGU and I were making some chai when we realized that something was wrong. We had just added milk, ginger, and cardamom.

Our milk had curdled.

It freaking looks like oatmeal.

Our milk was fine, so its expiration was out of the question. Why was it that all the other times we made chai, it turned out fine until now?

Well, it turns out we had taken a shortcut: in trying to release all the spices, we decided to blend the cardamom and ginger with the milk, and then add it to the rest of the pot, where water and milk was boiling. It seemed reasonable, right?

Well, perhaps not. It turns out that we may have not only added more milk than water -- effectively increasing the concentration of milk -- but that using the blender did more harm than good. According to this site, it's a bad idea. When the pGU's housemate makes chai, she doesn't blend anything, but just cuts it and boils it.

We know the milk must have changed pH to lead to this curdling, but how should we have avoided it?

The site suggests that what we should have done was to first bring 1 cup of water and 1/2 inch of fresh ginger (peeled and grated) to a boil. Then we should add 1 T of black tea, 1 cup of milk, and 1/2 T of cardamom. (And if you wanna go super exotic, saffron, cloves, cinnamon, and nutmeg can also be added.)

AHA.

Boiling the milk with the ginger causes the chai to curdle. We blended the ginger (even worse, we really caused a drastic change in pH) with lots of milk -- or at least more milk than the usual proportion of water.

And thus, a lesson in food chemistry: the pH of fresh ginger is somewhere between 5.5 and 6.5, which is rather acidic. Milk, on the other hand, is 87% water, but is slightly acidic at a pH somewhere between 6.5 and 6.7 when fresh.

At this pH, the milk phosphoprotein casein has a negative charge, and the casein micelles are relatively soluble, as they repel each other. However, in acidic conditions (like when we added loads of blended ginger), the milk coagulates. This is because casein has an isoelectric point at the pH 4.6 -- the point at which the number of positive charges is equal to the number of negative charges.
You can imagine that now, the positive part of each micelle is attracted to the negative part of the other micelles. This leads to the formation of ionic bonds among the micelles, which works against the dipole-dipole bonds of water. As a result, the protein then precipitates from the former colloid of milk.

What is now left in the curdled milk is precipitated demineralized casein and a solution of soluble calcium salts.

....and NOW you KNOW!

(And now we know that we should boil the milk and water/ginger separately, especially if we plan to use the blender...)

A pig disguised as a ginger root (disguised as a pig)

2010-02-01T21:37:00.005-05:00

I even scared the pGU with this .gif animation. I can't help it, though -- making them is so addictive.

I think my boring blog is now 50x more likely to put some unfortunate soul into an epileptic fit.

I have just discredited myself. (And my last post.)

2010-02-01T19:51:00.003-05:00

I went to my third rotation lab, was introduced to a PhD student (Korean, but in a graduate program at Cologne) and was told that I was an incoming rotation student in the lab.

He then asked me if I was an undergraduate. (Oh, and I mentioned he's Asian, right?)

This is not me. Contrary to popular belief, I am not white.

So let's see what the age difference is between the statuses I've been mistaken for from the beginning to the end of the day.

An hour ago, I was mistaken as an undergraduate, while in the morning I was mistaken as a post-doc. An incoming undergraduate is usually 18 years old, whereas a post-doc is usually anywhere from 27-35 years old. Granted, I most likely looked like a young (and spacey) post-doc. This leaves a potential 17-year range that I can pass for.

This is still not as bad as when I was a high school research student at a nearby hospital. When I went to my high school's administrative office (and I was in 11th grade), I was mistaken for a very lost and confused middle schooler. The average middle school student is 12 years old. However, when I was in the lab (and I wore a labcoat, which I owned and on whose breast-pocket I sewed my last name in Chinese!), I was asked by some chemistry post-docs if I was an MD/PhD student.

Now, if I were an MD/PhD student (and that would have been through NYIT's program), I would have been anywhere from 22-35 years old. Granted, I probably also looked like a young MD/PhD student, but the person who asked me this was Asian (more specifically, Indian.)

Why wasn't there a Doogie Howser, Ph.D? Obvious prejudices.

Dude, that's potentially a 23 year spread! I should have gotten my fake IDs earlier.

FYI: I don't drink. (That statement is mostly correct.) In that sense, I could have been a Mormon. Or Muslim. Did you realize that those two words both begin with "M" and are six-letters? Yes, I have problems.

We'll see how much this Asian age factor helps after I've aged a real 20 years during the sixth year of my graduate work.

On an ordinary day in lab

2010-02-01T15:47:00.003-05:00

Today, one of the MD/PhD students who graduated the lab just came back. I had taken over the desk (or rather, CB told me I was allowed to swarm over the space), so when the student came back to find her desk completely changed, she asked if I was a new post-doc.

This could mean many things, such as:

(1) She guessed this so as not to offend me if I were a post-doc. I suppose a post-doc who looks like grad student is worse than a grad student who looks like post-doc. Well, it's a lot better than mistaking faculty for students, which has happened at least twice in my presence.

(2) Maybe this haircut does make me look older.

(3) You really can't tell with Asians anyway, so you might as well flip a coin.

Maybe not like this.

(4) In my four months of graduate school, I've aged considerably.

(5) I should probably stop wearing so much gray-colored clothing.

(6) Wait a minute: the bright pink pig calendar on my desk didn't give away the fact that I'm a rotating grad student?

My calendar's pig is MUCH cuter than Sanrio's "Pippo" though.

Okay, back to work. The video really is coming....I assure you.

Too much fun this weekend...

2010-02-01T11:45:00.007-05:00

I think that it'll be impossible for me to blog about the entire Immunology Interview Weekend in one blog (it'll bore people to death...) so I'm considering in my next post to make a video showcasing (urr, sort of) the weekend.

It'll probably be embarrassing, strange, and quirky. Apologies in advance.

In addition, I may add a few comments about the weekend anyway under the video. Since we followed pretty much the same schedule as last year's, I may not talk too much about what exactly we all did, but other random things.

Until then, here's a gif that I created with the help of the pGU. The pGU recently bought a digital SLR (Canon xS) and has been playing with it all weekend. I came up with the idea of making the foaming fish spew out the MIT Brass Rat, but the pGU came up with the eerie light.

So until that video comes out, I give you...the "BLERGHHH!" fish.

We're a bit early for Halloween this year.

Real graduate students in the program are normal, I swear.

Social networks and interconnectedness

2010-01-31T14:41:00.007-05:00

I was kind of inspired recently at the Harvard Immunology Recruitment 2010 (which I will blog about!...later) at the idea of connectedness and how within a given environment, there are multiple ways of someone to be "related" to someone. It's even better than that whole six degrees of separation idea.

I noticed this when we were sitting at The Squealing Pig, and Karolina was sitting next to Jenna. Karolina was my buddy from last year, when I was interviewing at the program, while Jenna was my buddy this year (she was interviewing for next year's incoming class). I made this point, and we agreed that they were "grand buddies."

In my undergrad, fraternities and sororities have assigned "bigs" (as in, big brother/big sister within the Greek system). It was therefore extremely common to hear people remark "Oh, did you know that Jenn is my big-big?", which means "my big sis' big sis" and even up to four degrees of "big-ness." (Which can be achieved and remembered, as long as people are in master's programs around the area.)

Nevertheless, the immunology folks were not fond of this whole big-big-big thing (it's not proper English anyway, but that was MIT.)

It was then that I realized that it's not easy to always trace a "lineage" within the interview-buddy system.

Take this diagram as an example.

One thing you'll notice about this family tree is that in parentheses, I've put the year in which these individuals interviewed for the program. So for me, I am listed as 2009. However, Karolina was an MSTP applicant, and therefore formally never had a year. Moreover, she never had a buddy: it simply wasn't in the program's style. You can thus consider Karolina's buddy family a "new" family.

Moving on, you'll see that because first year grad student (G1) as well as G2 students take buddies, there is an interesting generational difference. I was sitting next to Lindsay, who is actually my former buddy's buddy. Does this make Lindsay my sibling-buddy? To Jenna, even though they're both recruits, they're actually a "generation" apart -- like a first-buddy-once-removed, or aunt-buddy?

There are also ways for a buddy-family to die. The saddest way is if the buddy doesn't come here for school (major sadness), but even though that limb of the buddy family tree dies off, you can grow more branches because you can always have another buddy.

The other reason a buddy-family may die out is that as buddies get older, they become busier (read: crotchety grad students) and don't come out. As a result, they take fewer buddies, and then you'll never have a first-buddy-once-removed and so forth. The up-side of this is that young, happy G1 buddies are always eager to take interviewees around, so the tree can flourish.

This will NOT be you at Harvard Immunology, I promise!

What makes this buddy tree most difficult is that everyone after several generations of trying to compile stuff forgets who their buddy's buddy was. In trying to compile, for instance, Teja's buddy family, I didn't know Matt's buddy when he was interviewing -- I don't think Teja remembers either. Moreover, Matt is swamped with work, so it looks like we won't send him an email inquiring about it anytime soon.

In furthering this investigation of connections (not the sketchy kind, but the inspiring kind), an appropriate example would be to look at the idea of mentorship. In the example of music, it's not uncommon for you to be able to trace your musical "lineage" to the great masters of all time.

For instance, Keith Underwood is my grand-teacher (my teacher's teacher), Jean-Pierre Rampal my great-grand teacher, and Isaac Stern my great-great-grand teacher. I am therefore the product of the products of the great.

This is fun to play around with, but not so meaningful in elucidating real connectedness. For this example, I give you my own family tree.

You'll have to open this in a new window. It's big.

I've boxed myself in a red rectangle. There are a few important (and fun) things to notice.

First, this is an incomplete family tree. Full of holes. This is because each one of these individuals has mentored countless other scientists, and this is good to note: it's that talent gives rise to more talent.

Another thing is the idea of mentorship incest. No, I don't mean that -- I mean the fact that mentors and their mentees sometimes mentor the same people. If you look at the tree (and this was drawn poorly, sorry), Ralph Steinman mentored MCN, and both of them mentored KL (who is doing EXTREMELY well in her post-doctoral studies). In this same vein, Prof. GWF is both my old roommate's mentor as well as grand-mentor.

The funniest thing is how everyone in academia is related. I don't just mean by looking at this diagram and seeing how the pGU is related to David Baltimore, or how I can claim several "greats" as my "great^n grand mentors." It was amusing for me to see that my old roommate and I have an immediate connection: FWA, who mentored my professor at MIT, and who mentored her professor at Stanford. This makes us "second-mentees," with FWA as a grand-mentor.

It's humbling to realize this, but also invigorating -- every student and aspiring scientist knows that they are the products of the products of great science, and that they too have the potential for the same. Connections are what they are, but continued mentorship is something completely separate and pivotal for this sort of ongoing development of talent and success.

We are the dust of stars, but we may be the stars themselves in due time.

Please do not anthropomorphize for this assignment

2010-01-25T21:46:00.003-05:00

"Having crossed the vascular walls, MBP–GFP T cells formed diverse contacts: some were short lasting (>10min), often serially involving several phagocytes, whereas others lasted for longer periods of time (Fig. 3a, Supplementary Fig. 9a and Supplementary Movie 9).

Notably, the duration of these contacts and the numbers of long-lasting arrests increased with ongoing inflammation (Fig. 3a)."

-Bartholomaeus et al., "Effector T cell interactions with meningeal vascular structures in nascent autoimmune CNS lesions."

I mean, honestly, what can we say? We're sketchy grad students.

New Year's Resolutions!

2010-01-25T14:27:00.004-05:00

I can't say that I'm the type of person who makes resolutions (urr, yeah, it's a little late to be blogging about them at the end of January), but I at least have some goals for 2010 and onwards. I think they're fairly achievable.

(1) Conserve more paper.
This can be achieved using a good pdf reader/annotator for discussions in class. At some point, I'll definitely need to print the papers out, but the feasibility of going paperless/green is increasing as I use Mendeley.

(2) Eat less.
When you eat at the cafeteria, you pay per ounce (44c/oz) and I am reminded each day that I eat a LOT of food for lunch. I think my goal should be anything below 0.6 lbs. Honestly, in this sense, the eye is bigger than the stomach. I am a pig.

Well, not quite like this.

(3) Eat more veggies and fruit.
This is related to #2. I really don't need to eat so much meat, so I should cut down on that and just eat more veggies and fruit -- yay! :)

(4) Be actively less shy.
Some people don't believe me when I say I'm pathologically quiet, but I am. This has to change if I want to get anything done in grad school. I'm the type of person who's actually afraid to ask for help. It's the sort of bad personality trait that has not benefited me in college and will surely not benefit me for the PhD. I have to force myself to do things that are good for me.

(5) Improve my time management skills.
Of which I have none. Instead, I have skills that allow me to be minimally competent in my classes. It's an art, but highly unproductive. This semester's classes will definitely require me to allocate time better (and probably necessarily sleep less). Starbucks will probably eat up my stipend as a result, which I suppose wouldn't be as bad if I owned Starbucks stock.

Coffeecoffeecoffeecoffee!

"Happy grad student" should be no oxymoron

2010-01-25T10:51:00.000-05:00

I just had a cup of coffee, which means I'm super-wired. The odd thing is that caffeine makes me blog. (I'd hate to see what would happen if I were on cannabis.)

Last week, I met with the lab members of a potential rotation lab. The PI was one of the scientists who helped pioneer and develop the use of high-throughput screens in the Arabidopsis and C. elegans, and currently works on in C. elegans. Additionally, he's one of the authors of Short Protocols in Molecular Biology (you know, that all-inclusive, comprehensive reference book you have in your lab.) You can imagine that he's a pretty awesome scientist, then.

However, I think one of the most memorable moments of this past semester was when I first met him (Prof. FMA) to talk about his lab, research, and a possible rotation. I told him that I was an immunology student interested in host-pathogen interactions, and wanted to learn more about how these different model organisms can be used to study innate immunity. He guessed that innate immunity at HMS was very mammalian-centered, and he was right.

There's a lot of oversight on the immunology student's part when we consider innate immunity. My old roommate and I used to think, "C. elegans? Do they even have an immune system? Why would anybody want to study worms? Honestly!" Looking back, this thinking is extremely naive, and essentially displays a sort of arrogance often seen in students concerned only with strictly biomedical research, and even more so, a lack of curiosity for core underpinnings of immunology and the real biology behind it.

Because this sort of thinking is probably more common than one would imagine (and hope), FMA and his colleagues have published quite a few reviews on how the study of innate immunity in C. elegans can grant us insight into innate immunity in higher organisms.

After I finish reading his reviews, maybe I'll post later about the implications of studying innate immunity in Drosophila, Arabidopsis and C. elegans, but for now, I just wanted to relate my anecdote about my initial meeting with Dr. FMA.

You can imagine it must be interesting for a molecular biology professor to be approached by a student in the immunology program. He was surprised that I made the trip not only to MGH, but also the day before Christmas Eve (oops), and probably that while I had some exposure to immunology (and primarily cellular immunology), I was very new to C. elegans and innate immunity.

And so, we spent about two hours talking about his lab's research, with me asking lots of basic questions about C. elegans and genetics. I told him that I didn't feel up-to-speed with molecular biology just yet, but that I was very willing to learn more. This led to me asking very basic questions, like, "If these worms are being infected by Pseudomonas as they eat them, they must have developed some way to distinguish their normal food bacteria (like non-pathogenic E. coli) from pathogenic organisms, right?"

When he told me that they did, and actually that they learned after getting "sick" from eating Pseudomonas, and avoided Pseudomonas next time -- very Pavlovian, right? I was really amazed and said that was really wild, and he replied enthusiastically, "Yeah, isn't it?! But it's neurobiology...and we actually don't do that."

What was really striking was that each time I asked some sort of basic, somewhat "trivial" question relating to using C. elegans as a system, he was always very patient explaining it to me. Questions like, "How exactly is a genetic screen done in C. elegans?" and questions about different techniques.

The best part about my meeting was when he said, "Hmm, so you wanna see the lab?" I got a personal tour of the lab from this PI, along the way bumping into JWS (one of the Nobel Prize Winners in Medicine and Physiology this past year) and GR (whose nickname seems to be "Nobel in Five [Years]" around campus. I got to see a C. elegans sorter (like a FACS machine, but for whole worms -- you can sort them by size and select for live ones!) and one of the plant rooms, where I finally got to see what Arabidopsis looks like (I know that's sad as a biologist, but sometimes you just never get a chance) and what happens to them when they're stressed, or treated with different plant growth hormones.

It was awesome.

I returned a month later to meet with the lab members, too...and almost felt like a post-doc when I visited -- I met with a bunch of the lab members and just got to chat with them. Dr. FMA had sent an email to the lab, saying something to the effect of, "We have a potential rotation student from Harvard Immunology. She's a first year graduate student. Please take some time out on Wednesday and sign up to meet with her on the sheet posted on the lab door."

And so, I got to meet lots of people from the lab -- an Infectious Disease fellow working on a model of candidiasis, a permanent researcher in the lab (who was Dr. FMA's former grad student, a current graduate student, some more researchers, and a post-doc (who noticed my brass rat and told me he had gone to MIT for grad school). All the lab members seemed exceedingly genial (and two post-docs who couldn't make their meetings sent other lab members to come find me and apologize on their behalf) and one of the post-docs I didn't get to meet emailed me and said that he'd be happy to answer any of my questions over the phone or in-person.

So what does it mean to be a happy grad student?

Comic from Natalie Dee.

To answer this question, you first need some certain level of introspection (omphaloskepsis) and decide for yourself what you want to accomplish from your PhD, what your goals are for the future (be somewhat realistic -- save your dream of being "that awesome Nobel-winning scientist for after you graduate) and what characteristics you want in a thesis lab.

For me, I think a thesis lab should provide me with a lot of resources -- not just physical ones, but post-docs who are not only extremely talented and knowledgeable, and professors who care about the research coming out of their lab, and who care a lot about the science. The lab environment's strength doesn't only lie in whether the lab goes on skiing trips together, or picnics, or other hangouts, but whether there is some greater sense of cohesiveness within the group.

And while it's not always possible to find a professor anywhere who has TONS of time to pore over each member of the lab and to "hold your hand" through your tough times in graduate school, what counts to me is that a professor's door is always open -- that if you want to talk about something, you can do that, and even multiple times a day.

Even if the office looks like this.

There are a lot of things that I learned from my experience in meeting with the members of this potential rotation lab, but I'll end with a piece of advice from another G1 in immunology. He worked in a very well-respected, big-name lab at Harvard for two years and said that a big portion of the reason for why he and the PI got along so well is because he actually didn't know the PI was a really important person.

He explained: "I mean, I just applied for this random job as a tech, went into his office and was joking around about stuff -- I didn't know he was someone that important. I didn't know that I was supposed to be a little scared to be there. And I think that's why I got along so well with him and would just go to his office when I was working there and talk about stuff."

There's certainly something to be said about one's comfort level with your professor. As one of the pGU's friends (who is on his way out from graduate school, and had good experiences) mentioned to me, it's essential to trust your mentor, because once that disappears, every day will be hell for you, and you'll only count the days and hours before you're out of there for good.

Maybe that's why I'm excited about working with worms for my rotation lab over the summer, too. I'm in an immunology program and don't know SQUAT about molecular biology, genetics, and C. elegans. I emailed a (very well-known, senior) professor and asked if I could talk to him about his lab and research, and he was not only welcoming, but extremely patient with me.

Well, we'll see where I land for a thesis lab in the fall. :)

Only so many things are pre-programmed

2010-01-25T09:37:00.000-05:00

Today, I was lamenting that because my paternal grandmother's father [great-grandfather] was adopted. This means I can no longer accurately trace my lineage.

"What do you care?" my mom said. "We all came from the same ancestor -- we're all from monkeys, anyway!"

The spirit of that, at least, was correct! I'm proud of my mom. :)

The interesting thing about how this factoid came about was because my dad was telling us how he had a whole SLEW of second-cousins who went to Harvard and MIT (Yale and other such schools were unfortunately not as impressive to the Chinese). This was especially impressive, given my family's socioeconomic background in the 1960's.

"So you do have smart genes somewhere!" my mom exclaimed to my dad.

And that was when she realized that these second cousins were really not "blood relatives." So while my dad's second cousins all went to the most desirable schools for any Chinese growing up in the '60s, my grandma's kids and her sibling's kids had a slightly different outcome.

My mom did, however, acknowledge that my dad's family must have had "hard-working" genes, since while it was a given that the Harvard and MIT second-cousins all had PhDs, MDs, and JDs, our side of the family has a PhD and now aspiring JDs and PhDs too.

I think, though, that while it really does seem like all my dad's second cousins have gone to top-notch schools (my cousin somewhat proudly told my dad "If I don't get into Cooper Union, I'm going to MIT" -- and he went to MIT later, when my dad hadn't even heard of Cooper Union), things are not so simple. Obviously "genes" (here used as some rather arbitrary contributer) are not the only factor.

I mean, otherwise these bibs would sell faster at the Co-op.

It is very likely that these second-cousins may have been better off financially -- they may have had some more parental guidance, more mentorship. They may have not had to worry strictly about supporting themselves financially in school, and may have had some important connections. The circumstances for each family may have just been so different that it's really impossible to assess what factors contributed to "success."

While I'm biased, I'm still happy the way things turned out. My mom may not think my dad has the "smart genes," but I think what matters most in the long-run is that the individual is passionate about his work, hard-working, and talented in it.

And this is very different from going to Harvard or MIT itself.

[This post was exhumed from a draft dated 8/16/09]

The problem with blogging

2010-01-22T18:02:00.005-05:00

There's a paradox about the idea of a blog itself.

Ideally, these are the things that one would like to achieve in a blog:

Experiment with new ideas
Express any idea freely (i.e., not have to worry about censorship)
Have a communication/conversation of such ideas
Obtain some sort of readership, however minimal

Unfortunately, to be able to do all these things is nearly impossible, and this is because with every action one takes, there is a consequence.

For instance, for someone to write like Pharyngula, several items have to be in order. Not only does he have to be able to be intelligent enough to synthesize such thoughts, but he has to be in a position in his career where what he says won't really affect what happens to him. For instance, if he's tenured (and a valuable member to the developmental biology department in his university), he won't have to worry about his inflammatory statements jeopardizing his career.

In my case, I have a lot of ideas, and they are crazy ideas, but they're not well-expressed. Moreover, sometimes because I'm not comfortable with making any particular case for myself (or expressing my opinion outright), I speak in circles and between lines. Most of the things that I mean to say just point to something random that I have noticed, with me wanting to say, "Hey, isn't that funny or interesting?"

Unfortunately, this is not always well-appreciated (one reason may be because my own understand of the way the world works is warped, and another may just be because I don't know what I'm doing most of the time), and it's not always a good idea for me to do this. As an example, I would have liked to post about how it seems that there are more "power couples" in immunology, but because I went about listing them (without thinking much of what it meant) instead of providing statistics (which are unavailable because it would simply be torturous to compile), I had to retract the post.

It's unfortunate to have to restrict oneself on one's own blog, but I think this is exactly where the paradox of blogging lies. You want readership, which then means you have to cull what you say. More readership, more curbing. If you kept a private blog or a diary via a Word document, you can say whatever you'd like.

Of course, no one would share with you your ideas (or bounce them back at you.)

The fact remains that there is no way for you to be completely free of such problems. It's absolutely inherent in the bounds that you have set for yourself and your goals for yourself.

In the end, you as a blogger must choose what is the appropriate repository for you thoughts -- whether it be in a public arena, or tucked away for private safekeeping in a dusty stash of drafts,

...or just something that you must let die because it's not worth the effort.

A day in the life.

2010-01-21T17:19:00.006-05:00

Broadly, my current rotation project investigates the role of the microbiome in gene expression profiles of a particular T cell subset. This means that I get to play around with bioinformatics tools and generate cool, colorful graphs.

This is a "volcano plot" (which I used to call a "lava plot," but only by mistake).

KABOOM!

Okay, so it doesn't look like a volcano plot when fold change is also on a log scale, but it's much more convenient to view the plot this way.

Maybe it looks more like a volcano plot like this?

Honestly, I think this should be renamed "fortune cookie plot."

See, recruits! I have posted. ^____________^;;

[PRIMAL SCREAM]

2010-01-21T16:46:00.005-05:00

I got this flier from an email sent to me by my oldest cousin. He, I think, knew that at some point I was interested in the whole Science vs. Faith topic (to which I've finally reached a somewhat-satisfying resolution), so he sent this to me and probably quite a few of his other friends who are in science.

This is where I started screaming "OH EM GEEEEEEE!!!" in my head.

Below is the letter, with my bolding and red-lettering.

My cousin sent me a PRO-CREATIONISM email!

------------------------------------------------------

Dear Friend,

Westminster Seminary will be hosting a Science and Faith Conference on March 12th and 13th, and would like to invite you to join us. This conference will be tackling some important questions: Are science and Faith compatible? What is the role of Christianity in the founding of modern science? How do we respond to the effect of Darwinism in our culture?

Speakers will include Dr. Vern Poythress, author of Redeeming Science; Dr. K. Scott Oliphint, author of Reasons for Faith; Dr. Stephen Meyer, author of Signature in the Cell: DNA and the Evidence for Intelligent Design; Dr. Jay Richards, co-author of The Privileged Planet: How Our Place in the Cosmos Is Designed For Discovery; Dr. C. John Collins, author of Science and Faith: Friends or Foes?; Dr. John West, author of Darwin Day in America: How Our Politics and Culture Have Been Dehumanized in the Name of Science; Dr. Bruce Gordon, co-editor of The Nature of Nature; and Dr. Paul Nelson.

This conference will be of special interest to anyone in church leadership, seminary and college students, or those involved in both a scientific and a Christian community. The speakers will be available during breaks to go into more detail about some of the issues and topics they will discuss, and on Saturday there will be a formal question and answer period during lunch.

You can register online at www.scienceandgod.org or by calling 1-817-923-1921, x2440. For each day there will be a box lunch available for an additional cost, with an option for a meat or a vegetarian meal.

For more information visit www.scienceandgod.org, or contact Janine Dixon, Discovery Institute, at jdixon@discovery.org or 1-800-685-0632 ext 108.

The Science and Faith Conference is sponsored by the Discovery Institute's Center for Science and Culture and Westminster Theological Seminary.

--------------------------------------------------------

My cousin sent me a PRO-CREATIONISM EMAIL!!! AAAAAAAAGHHHHH!!!

Yeah, to save myself from a big mess, I didn't reply (although the pGU probably wanted me to at least clarify what this email was really about.)

Oh well. ^________^;;;

Methods to scare your PI, #84021

2010-01-21T16:36:00.002-05:00

Last week, I was standing next to the coffee machine near the lab, where a graduate student and post-doc had already congregated. While making my coffee, one of the PIs of my lab was shocked to find that I was making some coffee.

"You got her hooked on it already!" he exclaimed.

"Oh no," I tried clarifying. "This is only my second cup of the day. I usually just have one."

Then the PIs voice drifted off as he walked away, remarking, "Oh, well! If it's going to be four of those sort of cups, then....!"

I didn't know what he meant, and one of the post-docs, seeing that I was a bit confused, said, "You do realize that this is an espresso machine..."

I said that yes, I did, but I always pushed the button for the "small coffee." It was then that he explained that pushing the "small coffee" button regulated the volume I was getting, NOT the concentration of coffee I was putting in my cup. My eyes widened in horror.

"Yeah, so the small coffee is about four espressos, so two cups is about eight espressos..."

This was when I realized:

[1] Why I had bad headaches/caffeine crashes in the afternoons.

[2] Why my PI was horrified that I was consuming so much coffee.

[3] Why it felt like I was burning a hole in my stomach each time I drank my meager cup.

(Oops.)

E-I-E-I-O!

2010-01-21T15:36:00.008-05:00

Some people like to summarize their weekends on their blogs, though I often have not. I think one reason is because I never intended to become so diary-like, but I figure that if the recruits really do bump into this blog, they ought to know that immunology students do have lives (albeit in my case, strange ones.)

Here is what the typical Harvard Immunology grad student's interests would look like in the BioBook, which we will be distributing to the recruits who are coming next week:

"What I do for Fun: Climbing, watching movies, going out and enjoying Boston nightlife, badminton, skiing, hiking, sports, exploring new recipes."

Something like that.

Here's mine:

"What I do for Fun: Blogging, Tae Kwon Do, chamber music, photography, exploring wildlife sanctuaries in Massachusetts, hiking."

Now, if I were really honest, this is what I would put:

"Reading pdfs on Mendeley, oding, watching Planet Earth, kicking people's butts (literally, not figuratively), finding new ways of conserving paper, photographing insects for my laptop screensaver to scare my labmates, drinking excessive espresso coffee, leisure reading, and torturing 30-year-olds."

I'll tell you guys the espresso story in the next post.

Last week, I went with the pGU and the pGU's cousin (c_pGU, cousin of the pGU) to go birding at Drumlin Farm, part of an Audubon natural reserve in Lincoln, MA.

It was lots of fun, though I hope the pGU and c_pGU were not too disappointed that we didn't do a lot of birdwatching. I got to try out my new pair of "butterfly" binoculars (a Pentax Papilio, something like this) and I'm finally getting better at using them. My improved use of the binoculars led to a skyrocketing appreciating of birding. (Yeah, I'm pathetic, but it was initially difficult and frustrating getting used to the binoculars.)

Nevertheless, we saw a lot of animals, and considering that I've never really seen sheep, goats, pigs, cows and chickens up close, it was a field day for me.

I've posted the pictures in this album and will let them tell the story for me.

I will say two quick things about my observations at the Drumlin Farm:

[1] Pigs are EXTREMELY heavy (and LONG!). The pGU, c_pGU and I got on a scale that would assess our weight in terms of a pig's weight -- that is, if there were a pig of your weight, what kind of pig would you be? All of us together still could not make a sow (we were still in "market pig" territory), but I will blame the fact that both of them are vegetarians(-ish). It's frightening when you realize that sows are probably at least 375 lbs.

[2] The funniest sight that I saw was of this sheep that was running. Sheep are actually quite big in reality. It was essentially a gigantic mass of gray wool on little, stumpy excuses of a black leg, chasing after another such large lump. And it made me really happy.

The thought of sheep running up and down the hill made me wonder whether pigs are still my favorite farm animals.

Photos courtesy of the c_pGU.

And I won't even be leaving Beantown for many more years

2010-01-20T09:05:00.002-05:00

How you know you've been in Boston too long, #4629:

You walk outside and exclaim, "Hey, it's really warm today!" when it's 33 degrees F outside with a high of 37.

I should count my blessing, though. Today, it's 22 degrees F in Minnesota, but it feels like 9 degrees! ^_______^;;

Hello, Harvard Immunology Interviewees!

2010-01-15T11:15:00.004-05:00

Last year, in preparation for the interview at Harvard Immunology, many of the recruits googled "Harvard Immunology" and instead of just finding the link to our program's website, found one of the grad students' blogs. It was a little strange for him because someone went up to him during interview weekend and said "Hey, I saw your blog! Cool pictures!"

Little did he know, practically every one of the recruits had done the same thing (though only one went up to him and told him.)

(By the way, you SHOULD check out Evan's blog, though. He shoots some beautiful photos.)

Meanwhile, I was an interviewee who posted about the weekend and my interview experience. Soon after, plenty of my fellow recruits (and future classmates!) saw the post. A few people were following the blog until they met me again in the fall for class. ^_____^;;

That said, I'm pretty darn sure that you've stumbled upon my blog for the same reason, and you may be an interviewee. (Let's face it, no one else reads this blog. The only other reason is that you are one of my close friends and I guilt-tripped you into subscribing!)

With that acknowledgment, it's probably time for me to do some real blogging. I don't guarantee that my blogging will actually make sense (or that it will be worth your reading), but given that potential recruits are reading this blog, I should at least:

(1) Stop posting random YouTube links. (I didn't have much to say. It's the lazy man's way of updating.)

(2) Say hello to the interviewees!

Yeah, so don't be shy if you're reading this and want to comment to say hello, even anonymously.

(Oh good grief, now I have to figure out what I'm actually going to blog about. Good thing I drank that espresso coffee today. If Red Bull gives you wings, this stuff certainly makes you feel like you're wearing a jetpack.

Something like this, more or less.

That, or I'm just gonna burn a hole through my stomach.)

(Thankfully)

2010-01-05T15:14:00.002-05:00

"Today, I ran from my desk, hurrying to go to my microarray analysis tutorial. I forgot to shut down my laptop before I left.

When I came back an hour later, the incriminating My Photos screensaver was on the screen, displaying my entire life embarrassingly as a slideshow for the entire lab to see. No one noticed or cared about it because they were either buried in science articles or focused on their computer screen. MLIL*

* My Life Is Lab."

"It is a truth universally acknowledged,

2010-01-05T15:07:00.003-05:00

...that a single Chinese post-doc in any given lab will gravitate towards the most proximal Chinese post-doc, and begin conversing in Mandarin."

Anyone who has worked in a lab will tell you that this is a natural law.

I was really supposed to be born 40 years before I actually was.

2010-01-02T22:40:00.002-05:00

Why? I totally missed:

1) Joan Baez
2) Bob Dylan
3) This song.

Isn't the xylophone at the beginning beautiful? ^______^

I do, in fact, believe this is how I see people

2009-12-31T00:56:00.004-05:00

So there's definitely some truth behind it!

Yay for Roald Dahl! (And thanks, MHC.)

Biology and art

2009-12-29T20:20:00.011-05:00

I went with my three younger cousins, uncle and aunt to the Guggenheim Museum in NYC. One of their big exhibits there is a comprehensive retrospective of Vasily Kandinsky's work. It was really interesting to see the progression of his style and work from his teens to right before he died -- from folk art-type paintings with the use of pointillism, to the very abstract and geometric, to experimentation with surrealism.

About ten years before his death, he became interested in incorporating ideas and forms from the natural sciences into his pieces. From the living room of his small apartment, he painted, but in this stage of his life, his formal vocabulary changed, featuring a softer palette and "biomorphic" forms -- as "informed by his contact with Surrealism, artists Jean Arp and Joan Miro, and his interest in the natural sciences."

He, in fact, started studying drawings and plates from botany, zoology and embryology. He incorporated amoeboid and cellular forms into his paintings, always swimming through light, gentle colors. A change from his previous, more geometic work, these forms now were more supple, suggesting microscopic organisms, while still expressing Kandinsky's inner life. He even mixed sand into his painting to give it a grainier texture.

As an example, here's Kandinksy's "Composition IX."

Kandinsky painted this while in Paris and is an example of the effect Surrealist imagery had on his artwork. There are biomorphic and geometrical shapes that float against the wide, highly-contrasting diagonal colored background. It's been remarked that the central form in the painting gives the impression of a human embryo in the womb.

This one (whose title I can't find) reminds me of an artist's rendition of what the inside of a cell might look like:

Here's another example of surrealistic biomorphism from Kandinsky's Paris period, painted in 1937, entitled "Capricious Forms."

This one reminds me of apoptotic blebbing.

Actually, looking at his paintings reminded me of Ernst Haeckel's Kunstformen der Natur (Artforms of Nature). While Kandinsky uses nature-forms in his art, Ernst Haeckel's lithographs, watercolors and sketches were meant to convey the beauty in these artforms of nature by detailing their symmetry and organization, especially with radiolarians.

Acanthophracta, a subclass of radiolarian protozoa.

For a cool documentary on Ernst Haeckel's life, work and philosophy, I highly recommend Proteus (2004), which I saw in a sort of "philosophy behind biology" class that I audited (well, I only went to the first three or so classes.) The beginning of the documentary is awesome, but be patient until 2:04 for my favorite part! ^____^

I found Kandinsky's work fascinating, even though it was tiring walking around the museum carrying my jacket and sweater, and getting a bit dizzy from walking the winding floors.

I never thought that I'd like abstract art as much as I did today. ^____^ WaHOO!

One of my favorite XKCD comics.

2009-12-19T12:46:00.002-05:00

I met Randall Munroe on Thursday night for a book signing put together by the MIT Press. This is the last comic in "xkcd: volume 0" and definitely one of my favorite ones.

This is ABSOLUTELY DISGUSTING!

2009-12-19T11:31:00.002-05:00

And it makes me so angry. I've seen all the crap that has been imposed on little children by religious, but this by far takes the cake. The other stories I've known can always be made analogous to "Santa"-like stories.

"God willing, we will all become like Wafa Idris. We will treat the wounded, and Allah will grant us martyrdom."

WHAT. THE. F***.

Ahaha, and it's listed as #666 too!

2009-11-23T21:20:00.003-05:00

Check out this xkcd comic. It's absolutely great.

Here's the first frame for you, just for a teaser.

Well...

2009-11-19T09:38:00.004-05:00

This is a lot more difficult than it sounds to do, but I like the idea.

Cubing >> Maggi

2009-11-15T13:50:00.007-05:00

So apparently there was an MIT Rubik's Cube Club that I never knew about during my years at undergrad.

"That's because you lived in McCormick."

Yeah, I know. You can shut up now. :)

The club hosted a competition yesterday that I heard about from my cousin, which sounded pretty awesome. Can you imagine solving a Rubik's Cube blindfolded? Insane.

As usual, that was not the point of this post. It was instead to add to my credentials of being the world's sketchiest grad student.

For that, I give you tips and guidelines to solving a Rubik's Cube by Rajiv Eranki.

In case you're confused why I'm posting this, let me help you. Follow these steps:

1. Focus all your perverted qi into the bolded, red words.

2. If you know my former roommate, you can pretend that you are imitating her voice while reading the text.

3. Practice saying this aloud to someone: this is absolutely essential. "Someone" may refer to your friend, colleague, mother, or even a random stranger.

4. Upon finishing reading aloud, ask your unfortunate listener for feedback on your oratory skills.

5. Thymocyte is not responsible for your face being bashed in as a result of your listener's taking offense.

Ready? Okay, so here it goes:

"Before extensive cubing, you may want to lubricate your cube so that turns are much smoother. You will need:

A lubricant. Petroleum Jelly works well.

Q-tips or tissue

Your cube.

To disassemble the cube, turn the top clockwise a bit so that the top face is about at a 30° angle to the lower two faces. Then turn the left face down. Eventually, if done right, one of the edges will pop out. Pulling out the remaining pieces is trivial.

After all the pieces are off the cube, coat all of the black spots of the pieces with Q-tips or tissues. To save your precious Vaseline, there really is no need to coat the interiors or to coat with huge globs. Remember to coat the core of your cube as well. Put the cube back together solved and you're ready to go. It should be assembled solved because chances are you'll assemble the cube with an unsolvable configuration (Murphy's Law)."

Figure 1. Yes, this is a real product.

Hey, don't shake your head at me. I'm pretty sure this was written with a certain frame of mind.

So!

Always remember to lube your cube. There are dire consequences awaiting those who fail to follow this simple rule.

It's not just me, right?

2009-11-10T12:17:00.006-05:00

The church that I attend has an interesting logo.

One Sunday, when I was staring at the program during the sermon, I noticed that the logo was somewhat interesting. It almost had some biological symbolism, albeit it wouldn't completely make sense.

So here's my interpretation.
Well, it wouldn't make sense why the HJ is on the outside of the cell. I suggest we put the cross a few inches below, at least.

Fuzzy biology. ^_______^

I love taking liberties!

2009-11-06T15:03:00.006-05:00

Before Molecular Biology class today, I didn't have enough time to make coffee, so I grabbed a cup from Boloco's (the hipster, slightly-overpriced burrito place nearby), since coffee there was cheaper than Starbucks. (It unfortunately also tastes cheaper.)

That aside, I was amused by what was on the paper cup itself. Notice the red boxed text below.

Nothing unusual aside from "be mindful," which just reminds me of immemor Theseus from that Catullus poem.

That was superfluous. Point, yes! What was interesting about the cup was its back.

What liberties -- Boloco is allowing me to set my own definitions for everything! I didn't know I had such rights.

Therefore, I went to the dictionary and examined all the definitions of "hot" that I could find, and came up with this list:

Yeah, there are a lot of definitions. Naturally, though, I had one in mind before running my search--

--and promptly added my preferred definition.

Because you decide what it means! :)

Ohhhhhh, NOW I get it!

2009-11-05T17:04:00.004-05:00

Introducing "Dr." Charlene Werner. She will explain to you the physics behind homeopathic medicine. (It involves a nearly mass-less universe, but LOTS of WATER.) I was somewhere between the "ROFL" state and the "I want to punch myself in the face" state while watching this. For a dose of rationality, I give you this site.

As PZ Myers has mentioned, the poor guy who uploaded the video seems to have been threatened with an impending lawsuit by someone affiliated with Charlene Werner. (Bummer.)

I hate it when people threaten, so I figured that I'd lend my meager blog space to promote the video. Copyright issues, my foot!

PZ said it best: "Welcome to the internet, Charlene."

A true ROFLMAOZzZ moment

2009-11-05T10:08:00.005-05:00

I received this important email in my inbox just now.

To: Residents of Vanderbilt Hall
From: Nancy Oriol
Re: Fire Alarms

The Boston Fire Department filed a complaint that many students did not evacuate Vanderbilt Hall appropriately during a recent fire alarm. They informed me that they have the right to arrest anyone who does not vacate.

The Fire Department is very concerned about our lack of responsiveness. No matter what the cause of the alarm, and even if you know the cause, you must follow the instructions given over the loudspeaker on your hallway and, if appropriate, evacuate until the Fire Department gives the all clear.

We know that evacuating can be disruptive, but it's the law, and the repercussions can be serious. And, most important, it can save your life and the lives of your colleagues.

>>LAWLZ! I would like to see some med students in cuffs. Sure, why not. ^_________^

I can sympathize a bit, though. I used to know people in my undergrad dorm who would just close and lock their doors and continue studying through the drill. Some things were just more important at the time.

A day in the life, Part 2.

2009-11-04T20:20:00.005-05:00

The med students took over the immunology students' conference room and filled it with the diagrams below.

The bottom diagram amuses me because our professor (who has, as everyone says to poke fun at me, "just an MD") asked us to draw this same picture and we (the immunology G1 students) failed miserably.

Had we been the ones using the board, you may have seen something unintelligible like this, which we drew on the board for our Wednesday Immunology Seminar class today.

We were discussing the Steve Reiner paper mentioned in the last post.

Just in case you were interested.

Fun article introductions in Science!

2009-11-04T09:29:00.008-05:00

While I was taking the bus from MIT back to HMS last night, I started reading a paper in preparation for our Wednesday Immunology Seminar. It's the March 2007 paper from Steve Reiner's group entitled "Asymmetric T Lymphocyte Division in the Initiation of Adaptive Immune Responses."

Essentially, the authors provide some evidence that after a T cell is primed, it will segregate proteins that mediate signaling so that proteins like LFA-1, CD8, CD3 will be polarized to one end of the cell. They believe that this is coordinated by APC-T cell interactions and that the first division leads to differential fating toward effector and memory lineages.

Okay, but my point here is not to comment about the paper (I can do that later, uh, after I finish reading the paper.) My aim was simply to show you how I misread the introduction.

So, already in the second paragraph of the page, I got stuck on the sentence and wondered for a bit too long whether it sounded funny to the ears of the reviewers too. That said, I think everyone is now familiar with my "het-erogeneous" misreadings and perversions of innocent, sweet stories of peoples honeymoons, printed on the back of Maggis.

It sort of begs the culminatingly annoying, but reputedly "most versatile joke on the planet."

("That's what she said.")

Though we may have to add this to the growing list of "That's what lymphocyte said" jokes.

>>Okay, but even if you think I have no life (I agree with that statement) and a very dirty mind (this statement is debatable...), I will tell you that my G1 friend Afro-Brown thought that that same exact line sounded a little different in her ears, too.

So, ha!-- I have company. ^____^;;

A dissection of my desk

2009-11-03T16:32:00.006-05:00

I've always believed that you can tell a lot about a person by looking at their desk and bookshelf. I did this comparison previously while I was in junior year of undergrad, but I've decided to undertake a more meaningful dissection of all things on and around my desk.

Figure 1. An atypical room. Inhabited by a graduate student living in a medical school dormitory (DMS 2016, ROFLMAO).

Here's the key:

A. "Think Pig" 2010 calendar, lovely birthday gift from the Bexlites.
B. A short collection of books that I brought from home to graduate school. I figured I really would have so little free time, it wasn't worth bringing even a sixth of my collection. I brought my non-fiction books.
C: Relevant undergraduate textbooks for reference.

D: The Greatest Show on Earth, the newest book by Richard Dawkins. (Lent to me by the pGU -- need to find time to read it.)
E: Miniature, inanimate pig farm.
F: Relevant graduate-level textbooks.
G: Binders for this semester.

H: Four year-old computer that I've had since the start of undergrad.
I: Ridiculously old iPod. It has all the songs that I've listened to since middle and high school. It's also on its last leg because it can't run on its own battery alone anymore.
J: A map of India, with all the labeled states. I wouldn't have known about its 28 states and 7 union territories otherwise. Yeah, be afraid.
K. It's pretty darn obvious I wasn't in the mood for doing work when I snapped this photo.

L. My "place mat." It's a small poster from BioLegend, which I got from the immunology retreat. I figured that if I had the T Follicular Helper Cell Pathway in front of me anytime I was at the computer, I had to absorb some information if I were bored and looked down at my wrists. Maybe.
M. A black and white photo of my dad and me. I'm not sure if it was taken on my birthday or his birthday, but it's a cheesecake. My mom snapped it. Unfortunately, I had it on my desk during all of undergrad, and my room in McCormick received direct sunlight, so it's been sunbleached. It's speckled with brown spots all over.
N. My trusty agenda book. I always bought the ones at the MIT Coop with our school seal. Now I have the HMS seal on my agenda book. You can also see that it serves as a make-shift mousepad. I don't have a real mouse pad, but am in desperate need of one.

I will be doing a Thymocyte Feature(!) on unsuspecting friends' desks, so stay tuned. >:)

Every morning when I wake, I thank God that I'm not a medical student.

2009-11-03T11:39:00.008-05:00

My G1 friend "Afro-Brown" and I found these two sheets on a table in the lounge on the fourth floor of our dorm (which is the med school dorm.)

The poor first year medical students at Harvard Medical School had their anatomy midterm last Friday (right before Halloween), so I'm pretty sure there was some crazy cramming going on right before then.

The pGU, upon seeing this, said facetiously "See how pathetic the first year medical student's life is?"

(Keep in mind that the pGU had to go through similar measures to memorize and cram for his medical school exams. I doubt he really means this 100%. Maybe.)

Apparently the use of mnemonic devices in studying for med school exams is not uncommon: the pGU's friends said that they did the same exact thing. I think when we showed them these sheets, it brought back memories of their own crazy (and perverted) mnemonic devices for studying. You can imagine that the more perverted the mnemonic device, the better it might be for memorization.

My favorites on the sheet are the femur/thigh "Pretty Girls Often Get Off Quickly" and the "C5-6-7 raise your wings up to heaven."

Figure 1. Long thoracic nerve roots (567) innervate Serratus anterior.

Actually, I just ran a google search for the latter mnemonic and found Mnemocine (cross mnemonics with medicine), which seems extremely useful for the (uhh, lazy and uncreative) medical student. Okay, I'm being harsh -- these classic ones seem quite good, but I think if you have a perverted enough mind (i.e., if you are me or my old roommate), you would have come up with some pretty sick mnemonics.

Then again, if they're catchy enough and spread like wildfire (viral medical mnemonics!), then they might end up on this site.

OH! And for the grad students who like to bash med students (we really shouldn't -- it's part of some inferiority complex that we ought not to feed, like MIT bashing Harvard over and over...), I give you this link: a mnemonic to memorize what northern, Southern, and western blots are used for. Evidently it's helpful for the USMLE (Step 1?).

Southern Northern O Western

DNA RNA O Protein

And that, folks, spells "snow drop."

Figure 2. A display of Snow Drop flowers.

Yeah, I know what you're thinking, but cut them some slack. I guess if you don't read papers day-in and day-out about these techniques, you'd need a mnemonic, too.

Figure 3. The S and "D in "snowdrop."

*************************
INTERACTIVE THYMOCYTE: If you are (or were!) a medical student and have a favorite mnemonic device you'd like to share, please post it as a comment to this blog post!
*************************

(...blah, but who am I kidding? I don't post enough interesting things to deserve readers, though everyone says that when they search "Harvard Immunology," they stumble across my blog. For some reason on my computer, when I do the same search, I don't see my blog pop up anywhere.

At least it's useful for this blog's small group of readers who forget the blog's URL and can just run a google search to find it again. ^_____^

How about a record collaboration with Shiv Pillai?

2009-11-02T10:08:00.004-05:00

These UCSD kids came up with new immunology-relevant lyrics to The Fray's "How To Save a Life."

It's quite good and the lyrics are funny, and here the are:

Project by Stephanie Hsi and Sidd Krishnamurthy

Video:
Red shirts - Pathogen
White shirt - Macrophage (Usually)
Black Shirt - T-Cell

Lyrics
Step one, you step on a sharp rock
You say oh well, it left such a small mark
But just that little bit of rust
Resulted in acquiring Tetanus

Onset of this of this infection
caused macrophage activation
NF-kB made IL 1, 6, TNFa
you begin to wonder why fever came.

What a poor defense, I'm feeling sick
Redness, swelling and tenderness
And I would have cleared it by now, abated
Had I been vaccinated

DC TLR 5 liked flagellin
And TLR 4 was LPS stalkin'
Try to slip past its defense
But antigens aren't innocent

Travel down the lymph nodes in a throng
B seven signals growing strong

And pray that T cells miss you
Yeahhhh, pray that T cells miss you

Why's this bond so strong, CD28
Costimulated and I just can't wait
To proliferate, differentiate
T-cells know how to save a life

As CD8 T-cells leave this place
It's finally time to make just one last choice
TH1 with IFN
Or TH2, IL-4 secretion?

He will do one of two things
He will support the macrophage
Or he'll play the B cell's game
CD40L will express all the same

B cells secrete IgM and D
recognizes the pathogen
AID help to class switch to IgG
Somatic Hypermutation
Complex forms between Ab-Ag
Complement flows surreptitiously
Punctures the membrane with all of its might
And attracts lots of phagocytes

I fell on to a knife
Let's do this one more time

Secondary response, I've got a friend
Plasma, antibodies, and memories
Soon I will clear this disease
Memory response, I do a dance
Damn pathogens don't stand a chance
And now I will stay up with you all night
Because my final is at 9...

A parking, I'll take the fine
If only I had more time

--------------------------------------

If you haven't heard Prof. Shiv Pillai's awesome raps and orations, see this link:

The lyrics are here.

Look what I found in the Hayden Library!

2009-11-02T09:18:00.006-05:00

It was being displayed on the side of a bookshelf and I spotted it while giving my cousin from New Jersey a tour of MIT.

Before you laugh, see these links: it makes sense, given the history of the squid giant axon. Three Nobel prizes came out of the use of research on squid axons for elucidating the action potential.

In 1963, the prize was awarded to scientists who discovered that charged ions traveling through the nerve membrane drive the steps of the action potential (Hodgins and Huxley).

In 1967, the Nobel Prize was awarded to a scientist who discovered the molecular pigments in the retina of many vertebrate and invertebrate eyes along with many of their properties (Wald). In 1971, scientists were awarded the prize for discovering that calcium triggers the repair of a damaged nerve (Katz).

For more movie clips, see this link.

Coooooooooooooooooooooool.

Sex @ MIT: THE SURVEY

2009-11-02T08:57:00.004-05:00

Earlier this month, The Tech, the student-run newspaper of my alma mater (man, it feels so weird to say that...) sent out a sex survey via email to all the undergraduates. They asked the students to respond with information about their sexual activity, the nature of that activity, and "how good it was." Apparently about forty percent, or 1729 people, responded.

http://tech.mit.edu/V129/N49/survey.html

I heard about this from my cousin and friends who are still at MIT. As they said, some results are far from surprising, and some...well, you'll just have to see for yourself.

I'm, of course, amused by the results of virginity by undergraduate dorm. McCormick (the all-girls dorm) naturally has the highest percentage -- 82.4%. Second place in this contest is Next House, with 70.0%. What do these dorms have in common?

LOTS OF ASIANS.

Speaking of which, this reminds me of this strange exchange between the pGU and me:

Thymocyte: "I never got to [insert some action word, I don't remember what.]"

pGU: "That's because you lived in McCormick."

Thymocyte, feigning anger: "Your house is McCormick!"

pGU: "Your face is McCormick!"

(....okay, moving on...)

Oh, and my major, which is chock-full of pre-meds? Course 7 (biology majors) are the 6th most chaste major, which means these future doctors are apparently get more action than chemistry, liberal arts, biological engineering and nuclear engineering majors!

Uhhh, which is what we would otherwise predict...?

Anyway, if you're interested in the pdf, it's here: http://tech.mit.edu/V129/PDF/N49.pdf

Wait, what?

2009-11-02T08:52:00.006-05:00

I saw this candy in the Chinese supermarket in Chinatown. The name is, well, uh --

See, I don't think this is what they had in mind when naming the candy:

...yeah, probably not.

Me & Meri "Bizarre Story Waali" MAGGI

2009-10-28T09:15:00.008-04:00

A few weeks ago, I got to try "Maggi" with the GSM (henceforth, he will be referred to as the pGU) and his best friend.

Maggi noodles are instant noodles, except that these were Indian-style ramen noodles, which meant that they were spicier and more fragrant. I noticed that on the package, Maggi was asking people to send in pictures of themselves. I assumed it was supposed to be pictures of them, having eaten Maggi, looking very happy. Maybe if you want to advertise for Maggi, you'd send in your picture, but why would you want all of India (plus the expats who eat Maggi outside of the subcontinent) staring at a picture of you while stirring their instant noodles?

That said, the pGU and friend suggested that I send in my picture. I would be hilarious if some obviously non-Indian person (Chinese!) were advertising Maggi noodles for the world. A riot, indeed.

Unfortunately, I never had the guts to send in pictures of me chomping down on Maggi noodles, and these people beat me to it.

This would be an interesting way of securing a marriage partner. Think! -- your picture is circulating all over the Maggi-eating world, and these people have got to be single (who else would send their picture, unless they were HUGE Maggi fans). It's got to be better than Shaadi.com!

The point is that there was also a section on the back for Maggi fans to send in their personal Maggi story. I nearly died from laughing when I read this one out. I'm wondering whether this person was aware of the thematic use of diction in her story. Either way, I'm sure the people at Maggi did, and they knew that printing the story would help Maggi noodles sell.

To get the full effect, I suggest you take the method that my old roommate used to, and pervertedly/seductively read the text below with a special emphasis on the red-colored words.

"Jyoti from Delhi - Me & Meri 'Honeymoon Waali' MAGGI

While on our honeymoon trip to Manali, I remember having a hot and soupy MAGGI with my husband, in the lap of the Himalayas. It was a really cosy and exciting experience. Thanks MAGGI, for making my honeymoon so memorable. I will always cherish these moments."

The pGU's friends take: "...Uhhhhh, it wasn't the Maggi's...."

Or was it? ;)

Random lolcat-inspired immunology!

2009-10-20T10:16:00.004-04:00

Or, "yes, I killed another hour." What have I done!?!

The original, inspired by my G1 Immunology friend, who described the caption as "that's what lymphocyte said."

It would look better as a single frame, which I was able to draw better than using this program.

Here's one based off of the NALP3 inflammasome. I thought it was appropriate, since NALP3 is also referred to as "cryopyrin."

If you're partial to NRI graphics like I am, then you might enjoy this one more:

Okay, now I really have to go back to work.

If only I actually had talent in drawing.

2009-10-20T09:17:00.005-04:00

Too bad I don't, though. I think that if I could draw to save my life, I would have a lot of bizarre ideas for an XKCD-like immunology cartoon.

Here's this idea, which I drafted during BCMP 200 Lecture. It's a reference to Dr. Tak Mak's (this year's Benacerraf Lecture Speaker) remark during the introduction to his talk, which was the idea that if an individual T cell clone never underwent apoptosis and just kept on proliferating, the entire earth would be full of T cells. Somehow, this idea (when pictured in one's mind) was more than amusing. It was just utterly bizarre.

And so, I wanted to draw the earth as a T cell. I couldn't quite do so without making it look really cartoonish (maybe that would be better?) and unfortunately, I just can't draw, period. Even worse, I foolishly deleted MS Paint from my computer (I loved MS Paint...), so I had to use RealWorld Paint (which sounds like some bad reality TV show about some promiscuous paint buckets.)

So here it goes. I need to employ an illustrator. Honestly, I think the idea would fly to make a good t-shirt out of it.

I couldn't resist trying to "lolcat" it a bit.

Feedback, people! I need feedback!

You know, an ordinary day.

2009-10-16T09:49:00.004-04:00

(Maybe.)

I meant to post this earlier, but I was pretty busy. I had gotten this in my inbox. I'm an ignoramus and only know Szostak as "that ribozyme guy," so this was cool for me. (Good birthday present.)

Congratulations Nobel Laureate Jack Szostak

Office of the Dean Mon, Oct 5, 2009 at 4:48 PM

Reply-To: Office of the Dean
To: ALLSTUDENT[at]listserv.med.harvard.edu

Dear members of the HMS community,

Today we are honored by the thrilling news that Jack Szostak, HMS professor of Genetics at Massachusetts General Hospital, has received the 2009 Nobel Prize in Physiology or Medicine, along with Elizabeth Blackburn and Carol Greider, for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase.

Jack has been a member of the Harvard medical faculty for 30 years, and he is the 13th HMS faculty member to win the Nobel Prize. He is a member of both the HMS Department of Genetics and the Mass General Department of Molecular Biology.

Jack's Nobel-winning research showcases the fundamental importance of basic science and how it can open up an entire field of investigation. His research focused on the stability of chromosomes in yeast cells. Working with Elizabeth Blackburn, he demonstrated that the sequences at the ends of chromosomes of one species could protect the chromosomes of a very distant species. Insightfully, he recognized that this implied the existence of an entirely new enzymatic activity in cells that function to protect the ends of chromosomes from degradation. This discovery, cited by the Nobel committee, has impacted our understanding of aging and led to potential treatments for cancer and other diseases.

By 1991, Jack shifted the entire focus of his lab to evolving new functional RNAs and other molecules in a test tube. To increase understanding of the earliest evolution of life, he is exploring the origins of functional biological macromolecules and membranes. Today, Jack’s main focus is the construction of a simple artificial cell that can grow and divide as well as evolve in a Darwinian sense to adapt to its changing environment.

I encourage you to read the Nobel announcement and the story of Jack’s work, which you can find on the Harvard Medical School home page: .

Please join me in congratulating Jack on this historic honor.

Sincerely,

Jeffrey S. Flier, MD
Dean, Faculty of Medicine
Harvard Medical School

-----------------

Just your typical day. :)

The Importance of Being Earnest (Johannes Walter version)

2009-10-16T08:48:00.005-04:00

It's been a while -- I've been "hosed," as we say at MIT. Grad school. ^_____^;;

So, two weeks ago on October 2nd, Prof. Johannes Walter gave us a research seminar lecture on "Proteolysis and the cell cycle regulation of DNA replication," but prefaced it with a rather inspiring "pep talk" on why we need to ask questions. So here is my abridged/accidentally re-interpreted version of what Prof. Walter said in class.

"In my field, I've met grad students, post-docs, and even faculty who don't ask questions in public -- ever. So before I begin, I'd like to give you a pep talk for asking questions.

So, why should you ask questions in a public setting?

First, you ask questions to satisfy your own curiosity. You want to know, and so you find you.

Second, if you don't ask questions, you're not giving feedback to the speaker, and that's not helpful for either the audience or the speaker. How is he to know where to improve?

Third, asking questions will get you noticed by people. I have read recommendations where it's written 'Not only is so-and-so a gifted scientist and thinker, but he is one of the few people in my department who asks questions at seminars.' It means you care.

And I've been on boards where we're hiring faculty, and the people on the board will ask, 'Does so-and-so participate in seminars?' They're asking, 'Is he a lively presence?'

Okay, so with that said, here are some pointers for the types of questions available for you to ask.

The Different Types of Questions
by Prof. Johannes Walter

1. The Well‐prefaced Technical Question: “We know that DNA binding proteins will interact with virtually any DNA sequence at low ionic strength. Therefore, I am wondering what salt concentration you use in the footprinting
Analysis.”

2. Clarification: “I didn’t understand how you were able to identify new ORC binding sites using chromatin immunoprecipitation analysis.”

3. Invite speculation/elaboration: “Can you speculate how Cdc45 might stimulate the MCM2‐7 helicase?”

4. The conceptual challenge: “You propose that MCM2‐7 participates in mitochondrial DNA replication, but it was my impression that this protein is exclusively nuclear.”

5. The data challenge: “I noticed that all the bands in your footprinting experiment seemed to become weaker upon addition of protein. Doesn't that suggest a non‐specific DNA binding mechanism?”

Different kinds of questions!

6. The “me too” comment: “We have done similar experiments and see very similar
Effects” or “We have done similar experiments, but get somewhat different results. In
our hands…”

Okay, so now that you know what questions you can ask, onto the seminar."

I found this "pep talk" particularly helpful to me. I tend to be painfully shy and quiet in many discussions, usually for at least one of these reasons:

(1) I think my contribution will be judged.
(2) I don't think my contribution is worth being uttered.
(3) I don't understand what's going on.

I think the sincerity and effort with which Prof. Johannes Walter explicated his opinion on the matter and encouraged us in the ways in which we can improve were almost moving. It reminded me of a very telling post that I found in junior year, when I wanted to try to understand why I was unable to participate in recitations.

It describes the "Peacock Syndrome." Fliptomato writes:

"[The physics students] seem to be obsessed about the image that they know what’s going on, even if this comes at the expense of actually knowing what’s going on.

To this extent, a physics student won’t ask questions in class. It would be terribly embarrassing if one asked a stupid question, because then everyone would know how stupid one is. So instead, physics students sit quietly and preen their feathers so they can cultivate their image.

This is stupid and harmful.

First of all, this is stupid because there’s a professor/TA who’s there to answer questions about physics. If you’re not going to ask questions and engage in discussions, then it’s a waste of time for everyone. You might as well quit university and learn physics by reading textbooks and watching online videos.

Secondly, it’s only going to get worse. This is like meeting someone and forgetting their name. You can ask again right away, or you can wait until you get to know each other more and then realize that now it’s really inappropriate to be asking their name. So suck up your pride and ask.

Thirdly, critical discussion is a different mode of thinking than passively listening to a lecture. You will learn more when you’re processing information in real time.

Science is all about asking questions. Learning how to ask good questions (and inevitably asking one or two embarrassing ones) is important."

A wise and astute commentary. It's very true: my lack of practice in asking and formulating questions has only been a detriment to my learning. Luckily, I became aware of the weakness (and there are many, many factors that have contributed to the weakness), but undoing it when you're in your first year of graduate school is difficult.

It's a shame to have to learn how to ask questions appropriately now, and to re-train yourself to think. Nevertheless, I think it can be done: step 1 for this semester is learning to be more shameless.

That's why I think the pointers that Prof. Walter has made clear are worth noting. I'm grateful that one of my grad school professors would go through the trouble to give us a "pep talk" before class.

It reinforces the notion that there just may be some hope for me.

Yeah, but would you get 72 of them? [EDIT]

2009-09-29T09:29:00.002-04:00

(They're a lot harder to come by, these days.)

Coldplay's lead vocalist Chris Martin, explaining the song lyric "I know Saint Peter won't call my name" from hit song "Viva La Vida" in an interview with Q magazine:

"It's about ... You're not on the list. I was a naughty boy. It's always fascinated me that idea of finishing your life and then being analyzed on it. And this idea runs throughout most religions.

That's why people blow up buildings. Because they think they're going to get lots of virgins. I always feel like saying, just join a band ...

That is the most frightening thing you could possibly say to somebody. Eternal damnation. I know about this stuff because I studied it. I was into it all. I know it. It's still mildly terrifying to me. And this is serious."

Anyway, the Christian imagery in the song is pretty interesting to analyze. My favorite lyrics, of course, are "Be my mirror, my sword and shield / My missionaries in a foreign field."

I'm behind on the times, so I only just started listening to it -- hah.

-------

EDIT: But since we're on the topic...

If I had to design my own heaven, it is going to be filled with the sound of angelic children in a choir singing emo songs.

Here's the existing prototype:

The harmonies for the chorus are beautiful, though. ;___;

And now, a public service announcement.

2009-09-25T16:01:00.004-04:00

I saw this piggy-rap/cartoon at every airport in China, but was never able to capture it on my video camera. I'm so glad other people managed to. My favorite part is the very beginning, so play close attention.

Swine influenza comes from America,
Spreads around the world.
Its true name is A(H1N1,)
What a shame!

And you've got to love the dancing female pig wearing the pink qipao in the background. It's kind of funny until it just becomes annoying.

Maybe I like it because it reminds me of this very funny video in Mandarin that pokes fun of every province in China (until they really bad-mouth the Japanese).

...or maybe it just has to do with my predilection for all things pig-related.

(Okay, back to immunology.)

A day in the life of...

2009-09-24T10:11:00.007-04:00

...a whiteboard in the immunology lecture room.

Overview (guest) lecture from Prof. Fritz Melchers.

Deprived or Depraved?: Tales from the SGS

2009-09-17T12:41:00.004-04:00

I was reading a paper for a discussion section in class today from Uli von Andrian's lab about the use of two-photon microscopy to study dendritic cells and naive T cells in order to understand more about T-cell priming.

I like to mark up my papers a lot, but got distracted for one second too long and went back to read the sentence preceding the one that I underlined.

And then I became ridiculously confused.

The abstract mentioned the displaying of erogenous behavior in mouse!?! I thought this was an immunology paper!

...urr, and that's when I realized it was just an aptly-hyphenated "het-erogeneous."

I think I'm on my way to becoming the sketchiest (if not the most vocal-about-my-sketchiness) grad student in the Boston area.

Anti-vaxxers in Boston, WT[]!?!

2009-09-15T12:06:00.009-04:00

This thymocyte message has been brought to you by the following letter:

Yes, the letter "F" is a good letter for beginning happy words like "flower" and "friend," but also for more appropriate words. You know, the angry, profane, four-lettered expletive kind.

The thymocyte is featuring this letter because of this picture, which I saw this Sunday.

From A Sunday in Boston

This was posted on the Harvard (Mass. Ave) Bridge. Absolutely nuts: I really didn't believe they'd come to Boston.

While it would be cool if all immunology grad students (well, we can fit in virology students, public health, medical students, etc. too) mobilized to drive the anti-vaxxers out of Boston, I have no idea how to even begin. Taking a lead from other cities/countries and posting vaccine information all over Boston would be a start, perhaps.

But really, it's sad to have this sort of problem in the first place. ;__;

I also have a feeling the anti-vaxxers who posted this particular flier are strongly associated with the anarchist/libertarian groups in the Boston-Cambridge area, though.

(Okay, back to paper reading.)

Why I Love MIT, Reason #3027

2009-09-14T22:23:00.004-04:00

Though I have grave doubts that the notes are actually correct, the attempt is still commendable.

Caption:

Early Wednesday morning, hackers installed seven notes on the great dome’s temporary scaffolding, commenting on its close resemblance to a musical score. The notes were the first seven of Rick Astley’s “Never Gonna Give You Up.”

I guess this is where professors "let loose"...

2009-09-14T13:27:00.003-04:00

The introduction to our Molecular Biology (BCMP 200) problem set. It's awfully reminiscent of the crazy sort of p-sets I saw at MIT, except this one is...well, some sort of noir humor, if you ask me.

I've italicized the stranger statements.

BCMP 200 Assignment 1 DNA Structure Module, Dr. W. Shih Due Tuesday September 15th, 2009, 5pm

You are Dr. Longwood, a scientist working in an parallel universe where George W. Bush has been elected to a third term in office, the Charles River is clean enough for safe swimming (even while you are sober), and everyone is required by law to belong to an a capella singing group (even after you graduate from college). You and your team have been contracted to work for an international conglomerate called Quad Enterprises at a scientific base in Bouvet Island, a small and uninhabited Norwegian island located in the South Atlantic Ocean. Your project is to characterize an archaeal DNA-binding protein (dubbed Loopium), derived from an indigenous microbe, that your team believes has potential as a nanoscale building block for self-assembling photosynthetic reaction centers that could offer dramatic improvements in the area of alternative-energy technologies.

Based on sequence homology, your team has discovered that Loopium is a homolog of nucleosomal proteins. One of your team members previously had been investigating the ability of Loopium to induce coiling in substrate DNA, but she recently was chipped away by an accident involving the Quad-Enterprises proprietary “Chip Chip Chip Chip” assay (how this assay works, and even its purpose, is confidential, and not relevant to our discussion here).

After a brief and tasteful funeral involving four-part close harmony, you now are trying to interpret results from her lab notebook regarding a recent experiment on in vitro binding, in the presence of Topoisomerase IB, of Loopium versus histones to a 7 kilobase pair plasmid isolated from E. coli. Proteins were stripped from the DNA prior to gel analysis. You see the figure below for an agarose gel stained with ethidium bromide after electrophoresis to visualize the DNA.

If I were writing a problem set, I'd spice it up a bit too. I can name at least one other person who would do the same (three-letter initial, I'll let you guess.) ^__________^

And speaking of spiced up, here's a picture taken from a Caribbean parade in Central Square. This large and ornate costume was one of my friend's favorites: he dubbed it "the turkey."

From A Sunday in Boston

You can see a plethora of such pictures (plus an umpteen more of garden flowers on Beacon Street) in the Picasa album.

Urr, back to p-setting. (It's like undergrad all over again, but luckily only for a year.)