Wednesday, April 20, 2011
Thursday, March 17, 2011
Curiouser and curiouser
To live is to choose. But to choose well, you must know who you are and what you stand for, where you want to go and why you want to get there.Kofi Annan(Ghanaian diplomat, seventh secretary-general of the United Nations, 2001 Nobel Peace Prize.)
This quote is stuck on my laptop desktop ever since I started grad school.
Who are you?
What do you stand for?
Where do you want to go?
Why do you want to get there?
"Who are YOU?" said the Caterpillar.This was not an encouraging opening for a conversation. Alice replied, rather shyly, "I--I hardly know, sir, just at present-- at least I know who I WAS when I got up this morning, but I think I must have been changed several times since then."
Basic questions under any kind of scenarios - so much so that it feels like a joke to be actually asking them. But I guess it is exactly because they are so fundamental, people miss them...
"I quite agree with you," said the Duchess; "and the moral of that is--'Be what you would seem to be'--or if you'd like it put more simply--'Never imagine yourself not to be otherwise than what it might appear to others that what you were or might have been was not otherwise than what you had been would have appeared to them to be otherwise.'""I think I should understand that better," Alice said very politely, "`if I had it written down: but I can't quite follow it as you say it."
I know enough of my strengths. I recognize and acknowledge my weaknesses. I wanna head in a certain general direction, but nothing more precise than that. Sometimes, when I get introspective, I mull over it and starts to end up in a circular thought...
`Would you tell me, please, which way I ought to go from here?'`That depends a good deal on where you want to get to,' said the Cat.`I don't much care where--' said Alice.`Then it doesn't matter which way you go,' said the Cat.`--so long as I get SOMEWHERE,' Alice added as an explanation.`Oh, you're sure to do that,' said the Cat, `if you only walk long enough.'
Many a times, I do not know where actually precisely I wanna go. Life can be like boxes of chocolates (instead of one) - spoilt for choices. But I know my preference, my idiosyncracies, my habits. Good choices or bad choices, they all add on to your experience. So that you know more of YOURSELF to choose again when you are faced another box of chocolates...
The White Rabbit put on his spectacles. "Where shall I begin, please your Majesty?" he asked."Begin at the beginning," the King said gravely, "and go on till you come to the end: then stop."Lewis Carroll "Alice in Wonderland"
Then I guess I will just trudge on ahead fearlessly.
Learning how to trust myself along the way.
Monday, February 14, 2011
My first attempt and experience at Scientific Journalism
Finally after 4 months of gestation, my very first tiny step in scientific journalism got accepted and is going to be published in the Yale Journal of Medicine and Biology. Another thing to add to my CV!! =)
But it was an interesting experience. The initial idea was actually to cover a symposium organized by the new Yale Institute of Systems Biology. But I ended up volunteering to interview the director of the new institute. It was really an enriching experience. The review process was gruelling though. It's not as bad as peer review research papers, but I did not agree with the reviewers at so many junctures that half-way through I wanted to just give up and not write anymore. Thankfully I pulled some late-nighters and pushed through. Hopefully it will be well-received by the general reader. Well, even if people don't read it, at least I got that out there.
Can't say I really like it. But it was an experience all the same. Thanks to all who gave me helpful comments and support!! Really appreciate them all!
Will update again when it gets officially published.
But it was an interesting experience. The initial idea was actually to cover a symposium organized by the new Yale Institute of Systems Biology. But I ended up volunteering to interview the director of the new institute. It was really an enriching experience. The review process was gruelling though. It's not as bad as peer review research papers, but I did not agree with the reviewers at so many junctures that half-way through I wanted to just give up and not write anymore. Thankfully I pulled some late-nighters and pushed through. Hopefully it will be well-received by the general reader. Well, even if people don't read it, at least I got that out there.
Can't say I really like it. But it was an experience all the same. Thanks to all who gave me helpful comments and support!! Really appreciate them all!
Will update again when it gets officially published.
Sunday, February 13, 2011
Documenting my 'seasons'
Sometimes, I feel I am like an insect (seriously, I once dreamt I was a cockroach... of all things... zzzz). There are certain parts of a cycle dedicated to certain activities: feeding, moulting, actively social...
I have an epiphany suddenly that I should try to document that. It should have been done eons ago given my self-discovery of such a characteristic. But I wasn't interested in spending my time on such a seemingly frivolous (or inane) activity. Right now, I think it will be interesting to see how my cycle changes and make observations. Also, to my own benefit, the predictability of such a cycle.
After the Winter Ball yesterday, I have decided to tag Feb as my 'unsocial' season. Using the months as a time gauge can be fallacious but good as a more intuitive demarcation method.
Month: Feb
'Unsocial' season
Defined by: outwardly obvious social awkwardness, the inability to engage in sensible conversations even within familiar cliques or on familiar topics, frequent mind-blanks and incompetent articulation of oneself. And lack of desire to take photos and be taken.
Remarks:
This might not be demarcated by months, but instead by some other factors TBC. This can also be a triggered effect. For instance, dancing next to a boombox can trigger a flight response. Then, it no longer can be classified as a seasonal habit. Further prospective and retrospective examinations are required.
The road to self-discovery is long and arduous indeed.
I have an epiphany suddenly that I should try to document that. It should have been done eons ago given my self-discovery of such a characteristic. But I wasn't interested in spending my time on such a seemingly frivolous (or inane) activity. Right now, I think it will be interesting to see how my cycle changes and make observations. Also, to my own benefit, the predictability of such a cycle.
After the Winter Ball yesterday, I have decided to tag Feb as my 'unsocial' season. Using the months as a time gauge can be fallacious but good as a more intuitive demarcation method.
Month: Feb
'Unsocial' season
Defined by: outwardly obvious social awkwardness, the inability to engage in sensible conversations even within familiar cliques or on familiar topics, frequent mind-blanks and incompetent articulation of oneself. And lack of desire to take photos and be taken.
Remarks:
This might not be demarcated by months, but instead by some other factors TBC. This can also be a triggered effect. For instance, dancing next to a boombox can trigger a flight response. Then, it no longer can be classified as a seasonal habit. Further prospective and retrospective examinations are required.
The road to self-discovery is long and arduous indeed.
Wednesday, February 9, 2011
Shuffling my routine
My current PI was playing squash in the courts. It was the weirdest feeling. Good thing I didn't play with him. I will not know what to do!! Damn... I will think about it when it happens.
I think I am losing some steam in playing squash... I need someone to train with. Or I need to some time to train myself... In any case, too much squash is no good too. I need to start moderating, before it starts jeopardizing my schedule.
I felt great today though. Played 12 matches and had a great workout. But I need to up my court fitness to derive more enjoyment out of these.
And I seriously need to think about my meals. I am doing a lot of weird dinner timings, and getting hungry, which I don't think it's good at all. I will try cooking in the morning and then saving for the evening. Think that might prove to be better.
Alright, J, chin up and good to go!
Monday, February 7, 2011
False positives
I tend to get afraid when people (especially undergrads) tend to have this idealized notion that whatever technology or methodology that has been invented is TRIED, TRUE and 100% ACCURATE.
This was one of the things I had to grapple with when I first realized that scientific papers can be deeply flawed and controversial during my undergrad days. Those were the days that you thought publications were the gospel truths, and held the answers to your assignments or projects. The public likes to believe scientists are at the top of the academic food chain, which basically generates the ideas that push the whole human society forward in science and technology. Those are true MOSTLY.
Now that I am deep within the realm of academic pursuits, it is probably more saddening personally to learn that people take things at face value (even more frightening is that I do that too). For example, Genome-wide association studies (GWAS) are NOT exactly genome-wide. They are SELECTED genome variations that spans the genome, biased towards certain regions of the genome. And the fact that GWAS relies heavily on probabilistic and statistical underpinnings imply a necessity for large sample sizes, often of the order of thousands. Anything smaller runs the risk of generating false positives. Even then, GWAS cannot detect everything. In fact, it doesn't. For starters, it only accounts for the common variations in the COMMON diseases. Those diseases that are of lower frequency, or have lower penetrance, are not detectable by GWAS, just because it is simply statistically not possible to do that at an optimally accurate level with insufficient sample size (funding) and coverage of the genome. In any case, GWAS have, IMO, failed on so many instances because of the large number of false positives and non-reproducible results generated.
If we want total "GWAS" studies, we would need sequencing. Even sequencing has its caveats. The sequencing technologies are moving fast to very accurate levels at a high throughput rate by parallel sequencing whole molecules. But currently most of the mature technologies work by finding a consensus signal from an amplification of the query genome and then aligning that to a reference genome, which is also really a consensus of several biased genomes. There has been many cases where amplification can cause ambiguous sequence generation (due to equal number of signals) and the reference genome contains sites which are actually rare (i.e. not typical of a "normal"/consensus genome) as compared to the general population (due to heterogeneity amongst humans).
What I want to emphasize here is not the fallacies of all science that has been done. But rather impress upon the idea that while science typically is based on STATISTICALLY sound observations, there are caveats everywhere. I still believe science working for us. But we definitely have to be cognizant of the pitfalls and underlying assumptions that we are making in order to make better decisions with regards to scientific issues. Because only then will we be able to weigh out the pros and cons to address the matter at hand most efficiently.
This was one of the things I had to grapple with when I first realized that scientific papers can be deeply flawed and controversial during my undergrad days. Those were the days that you thought publications were the gospel truths, and held the answers to your assignments or projects. The public likes to believe scientists are at the top of the academic food chain, which basically generates the ideas that push the whole human society forward in science and technology. Those are true MOSTLY.
Now that I am deep within the realm of academic pursuits, it is probably more saddening personally to learn that people take things at face value (even more frightening is that I do that too). For example, Genome-wide association studies (GWAS) are NOT exactly genome-wide. They are SELECTED genome variations that spans the genome, biased towards certain regions of the genome. And the fact that GWAS relies heavily on probabilistic and statistical underpinnings imply a necessity for large sample sizes, often of the order of thousands. Anything smaller runs the risk of generating false positives. Even then, GWAS cannot detect everything. In fact, it doesn't. For starters, it only accounts for the common variations in the COMMON diseases. Those diseases that are of lower frequency, or have lower penetrance, are not detectable by GWAS, just because it is simply statistically not possible to do that at an optimally accurate level with insufficient sample size (funding) and coverage of the genome. In any case, GWAS have, IMO, failed on so many instances because of the large number of false positives and non-reproducible results generated.
If we want total "GWAS" studies, we would need sequencing. Even sequencing has its caveats. The sequencing technologies are moving fast to very accurate levels at a high throughput rate by parallel sequencing whole molecules. But currently most of the mature technologies work by finding a consensus signal from an amplification of the query genome and then aligning that to a reference genome, which is also really a consensus of several biased genomes. There has been many cases where amplification can cause ambiguous sequence generation (due to equal number of signals) and the reference genome contains sites which are actually rare (i.e. not typical of a "normal"/consensus genome) as compared to the general population (due to heterogeneity amongst humans).
What I want to emphasize here is not the fallacies of all science that has been done. But rather impress upon the idea that while science typically is based on STATISTICALLY sound observations, there are caveats everywhere. I still believe science working for us. But we definitely have to be cognizant of the pitfalls and underlying assumptions that we are making in order to make better decisions with regards to scientific issues. Because only then will we be able to weigh out the pros and cons to address the matter at hand most efficiently.
Sunday, February 6, 2011
Recruiting weekend
I have never done a recruiting weekend before. This was something that bugged me as well. Like international students were not always invited I guess. There were 14 prospective students for this year from all over US. I volunteered to go for the GYPSCY event and the dinner at Geronimo's (which according to Emm serves southwestern American cuisine - nachos and bean-based).
It turned out I was seated in between 2 of the prospectives at Geronimo's. Probably they were tired, because they didn't seem very interactive at first. I didn't know how to continue a conversation that involves minimal input from the opposite end. Thank goodness Emm and Bec were sitting nearby and we were all kind of drawn to their conversations. Emm and Bec are really good at chatting. I have long acknowledged that I probably will not master the art of schmoozing during this lifetime, but I thought I might have improved just a teeny little bit since I arrived in the US. Apparently that tad bit wasn't measuring up to the expectations of the occasion, what with exhausted minds and an inept schmoozer LOLX.
Maybe I was tired too, talking without thinking much. Some of my worst articulation yet. But well, I get affected by the vibes of the circumstances pretty easily... Excuses? Probably. Still, I will like to think the night was surprisingly a more retrospectively-fulfilling night of self-discovery, than it was when I was there, and seeing everybody engage in vivacious conversations, while I am struggling to keep myself rooted to that chair.
I also felt a little sensitive to the fact that every time I mention to some people (let me emphasize, NOT all, just some) I am from Singapore, there is this momentary hesitation on the other side of the conversation. Brief but palpable. Like perhaps they were hoping I am from some God-forsaken corner in the US with some undiscovered mixed accent and not some non-US Asian ("alien" as they call non-residents in legal lingo). I swear I can literally hear a "click" sound in the background when they made that connection between "accent" and "Asian". Haha. A little touchy there, self-deprecating even, but I ought to be at peace with and rise above such things now, after some (again, it's SOME, and I really like Germany alot) ordeals I had in Germany. *lame J*
Will love to know the people a little more, not only the new people but the old acquaintances at the table as well. But I guess sometimes, it takes more than just mere talking to get connected.
The food at Geronimo's was cool though. The desserts were pretty interesting - a spicy chocolate (from chipotle) and lime tequila tarts. Next time can probably bring XL to that side of town for some nice fancy restaurants.
It turned out I was seated in between 2 of the prospectives at Geronimo's. Probably they were tired, because they didn't seem very interactive at first. I didn't know how to continue a conversation that involves minimal input from the opposite end. Thank goodness Emm and Bec were sitting nearby and we were all kind of drawn to their conversations. Emm and Bec are really good at chatting. I have long acknowledged that I probably will not master the art of schmoozing during this lifetime, but I thought I might have improved just a teeny little bit since I arrived in the US. Apparently that tad bit wasn't measuring up to the expectations of the occasion, what with exhausted minds and an inept schmoozer LOLX.
Maybe I was tired too, talking without thinking much. Some of my worst articulation yet. But well, I get affected by the vibes of the circumstances pretty easily... Excuses? Probably. Still, I will like to think the night was surprisingly a more retrospectively-fulfilling night of self-discovery, than it was when I was there, and seeing everybody engage in vivacious conversations, while I am struggling to keep myself rooted to that chair.
I also felt a little sensitive to the fact that every time I mention to some people (let me emphasize, NOT all, just some) I am from Singapore, there is this momentary hesitation on the other side of the conversation. Brief but palpable. Like perhaps they were hoping I am from some God-forsaken corner in the US with some undiscovered mixed accent and not some non-US Asian ("alien" as they call non-residents in legal lingo). I swear I can literally hear a "click" sound in the background when they made that connection between "accent" and "Asian". Haha. A little touchy there, self-deprecating even, but I ought to be at peace with and rise above such things now, after some (again, it's SOME, and I really like Germany alot) ordeals I had in Germany. *lame J*
Will love to know the people a little more, not only the new people but the old acquaintances at the table as well. But I guess sometimes, it takes more than just mere talking to get connected.
The food at Geronimo's was cool though. The desserts were pretty interesting - a spicy chocolate (from chipotle) and lime tequila tarts. Next time can probably bring XL to that side of town for some nice fancy restaurants.
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