Another year, another poster presentation and another disappointment at not having won anything.
I understand that this department can't give me a prize because I don't technically belong to it. But I really don't understand why they force me to participate, raise my hopes and then dash them to the ground every year.
Fine. Keep your stupid money, people.
Projects that will always get awarded: vaccine work/ work on therapeutic drugs, even though each of them may be more cytotoxic than not (and they will be awarded despite the fact there's data on the poster showing that they are cytotoxic). Basic research on vaccines and therapeutics is a) repetitive and b) totally random in the case of drugs- you pick a drug from a million screens, and you hope it will work. Vaccine design, at least, has some elegance to it.
Projects that will always be second best: work on host restriction factors. Host restriction factors, in my mind, are so beautiful. They build such a lovely story of the evolving immune system, of the ever-present combat between microbes and the immune cells, of adaptability of systems and of nature, as a whole. Of course, I am biased.
Projects that judges will always shy away from: mine :(
Thus, I wallow in self pity.
My project is on something people discovered 24 years ago, have figured out a lot of things about, but cannot figure out exactly what it is. After 24 years of ifs, buts and maybes, nobody wants to touch the stuff any more.
Hey. Writing this up has suddenly given me some insight into myself: maybe the reason I've been so wary of doing basic science in the future is because of my PhD project. If I were to pick a project in the future, I would not pick one that is so nebulous, so prone to variation between humans, between systems and between cells. Because when something is that wishy washy, you stop believing in it.
Somehow, I have to finish up this PhD. Then, I need to do something that will give me some results within a reasonable period of time and with reasonable amounts of energy. Something that works beautifully and consistently. Because this project is slowly draining me out of all my optimism and love for science and research. Because I know that it is time to call it quits, wrap it up, dust my hands and say, "Enough".
Friday, September 17, 2010
Buried Deep Within
We had our first organized lab clean-up in.... wait, can you take a guess as to how many days/months/years? Hmm... one semester?? NO! One year?? (Not a bad guess given that we have an annual lab inspection and we have passed it every year).... NO! First time since I have joined the lab, which was 4 years ago?? NO!
Okay, this could go on forever. I'll give you the answer:
It was the first time EVER!!! In, give or take a decade, 3 DECADES!!
Guess what we unearthed?
-->Bags of cotton autoclaved in 1990- with the autoclave tape slowly crumbling to dust and the cotton getting the consistency of cotton candy
--> pH meter from the 80's era
--> Media from 2001 (someone has been very carefully storing that media for close to a decade now, without ever using it.... and not even the least bit of fungal growth in it. Surprising, no?)
--> Lab notes. Dozens and dozens of books of former grad students, sitting around smugly. It is always fun to read bits and parts of other people's lab notes. In the initial, innocent years of research, lab notes are serious tomes, focused only on science. By the final year, lab notes are insouciant. And wedged in between experiments are grocery lists, monthly finances and, if the student is female, menus and recipes.
--> The coup de grace... hold your breath.... Tritium!!! It was sitting inside a little glass vial, looking, for all the world, like some harmless cytokine which somebody forgot to return to the fridge. I picked it up and shook it, because it seemed a bit thick and yellow. Then my brain rather slowly registered the words "3H isotope". "Maybe all 3H is not radioactive?" I was thinking because this vial looked so innocuous. Then I turned it around and there was the orange sign with the words "Caution! Radioactive Isotope!" written on it. Yikes!
I used the cotton-candy to wrap up the vial, Lori stuffed it into a tin (couldn't find lead) box and Kathy found us a Geiger counter. Poof! No counts registered- we probably were at more risk from the radon in the room than anything in that vial. Good thing too... even though it makes a boring end to what could have been a sensational story. Our lab would have got into SOO much shit otherwise. I wonder how old it is... the lab stopped registering as a radioactive isotope-user nearly 10 years ago.
Anyway, half life of tritium apparently is only about 7 days. So, it couldn't have been radioactive for very long after it was bought.
This cleaning session was only 3 hours (for which I was late, as usual. But only by half an hour!). I wonder if we will have the energy and motivation to continue cleaning next week or the week after. After all, there are still EIGHT more lab rooms that belong to us and that probably need to be cleaned :s
Okay, this could go on forever. I'll give you the answer:
It was the first time EVER!!! In, give or take a decade, 3 DECADES!!
Guess what we unearthed?
-->Bags of cotton autoclaved in 1990- with the autoclave tape slowly crumbling to dust and the cotton getting the consistency of cotton candy
--> pH meter from the 80's era
--> Media from 2001 (someone has been very carefully storing that media for close to a decade now, without ever using it.... and not even the least bit of fungal growth in it. Surprising, no?)
--> Lab notes. Dozens and dozens of books of former grad students, sitting around smugly. It is always fun to read bits and parts of other people's lab notes. In the initial, innocent years of research, lab notes are serious tomes, focused only on science. By the final year, lab notes are insouciant. And wedged in between experiments are grocery lists, monthly finances and, if the student is female, menus and recipes.
--> The coup de grace... hold your breath.... Tritium!!! It was sitting inside a little glass vial, looking, for all the world, like some harmless cytokine which somebody forgot to return to the fridge. I picked it up and shook it, because it seemed a bit thick and yellow. Then my brain rather slowly registered the words "3H isotope". "Maybe all 3H is not radioactive?" I was thinking because this vial looked so innocuous. Then I turned it around and there was the orange sign with the words "Caution! Radioactive Isotope!" written on it. Yikes!
I used the cotton-candy to wrap up the vial, Lori stuffed it into a tin (couldn't find lead) box and Kathy found us a Geiger counter. Poof! No counts registered- we probably were at more risk from the radon in the room than anything in that vial. Good thing too... even though it makes a boring end to what could have been a sensational story. Our lab would have got into SOO much shit otherwise. I wonder how old it is... the lab stopped registering as a radioactive isotope-user nearly 10 years ago.
Anyway, half life of tritium apparently is only about 7 days. So, it couldn't have been radioactive for very long after it was bought.
This cleaning session was only 3 hours (for which I was late, as usual. But only by half an hour!). I wonder if we will have the energy and motivation to continue cleaning next week or the week after. After all, there are still EIGHT more lab rooms that belong to us and that probably need to be cleaned :s
Friday, August 27, 2010
Tamil-English Part 1
Thanks to my friend, Mangai, I no longer have to struggle to figure out what to write on this blog. Fungi-Mangai, for that has been her nickname since the time we first met in the dusty classrooms of Alagappa Chettiar College of Technology more than 9 years ago, has a blog: http://rainbows-ahead.blogspot.com/
She's got into the habit of blogging once in a while in Tamil. I've got into the habit of reading, very laboriously, these Tamil blog-posts. Why do I love reading her Tamil blogs? For one thing, it is the type of Tamil I more or less understand, rather than the high falootin', literary type of Tamil in textbooks. Plus, she uses English words once in a while, which I grab on to with the fervor of a novice swimmer being thrown a lifeline while swimming in deep waters.
Anyway, the first post I read is called "Chennai". Lovely! Land of my heart (and pools of my sweat!), how I miss you! I know why she wrote about Chennai. There was a reunion of our batch from the above-mentioned AC Tech on the 15th of August this year and she had attended it. When I say "our batch", I don't just mean our class of 50 from the Biotechnology course. I mean, our batch of more than 200, who belonged to Leather Tech, Textile Tech, Chem Engg and Biotech. We had classes, all 200 of us crammed into one large (and dusty, as previously noted) room together, in our first semester. What were these classes, you ask? How could all these disparate courses have anything in common? Well, you're right. They don't. That's why we took classes in subjects that had nothing to do with any of these subjects, but that were considered mandatory for anybody graduating with an engineering degree. Weird, no?
These core classes were: Engineering Mechanics, Engineering Drawing, Physics, Advanced Mathematics, Technical English, and worst of all, Workshop, which consisted of 1.5 months each of Filing, Welding and Carpentry. Well, to be honest, Workshop was kind of fun. It was the viva-voce examination in Workshop that was truly terrible. I was rather good at filing, welding was a piece of cake- the instructor would come and hold your hand (if you were a girl, that is) and do the welding (he liked holding girls' hands.... we didn't mind, since we could get out of the class quickly. Boys had to wait in line, till we girls finished "welding" and then had to do the stuff by themselves. It was not easy being a girl in Chennai, but there were advantages)- and carpentry was the worst. You had to pick a piece of wood, saw it to the right size, file (or something like that) THAT to make it look neat, and then saw it to make all sorts of joints- T joint is the only one I recall. Anyway, that was not fun. A classmate called Mohammed, God bless him, helped me do all my carpentry- "help" meaning that I would pick my piece of wood and struggle with doing anything with it for the whole hour of the class, then he would come by, and do whatever had to be done with it in 15 minutes and hand it in under my name. Nice of him.
In addition to these classes, we all had to choose one of the following- National Social Service, National Cadet Corps or National Sports Organization- to be a part of, for one year. Most of us lazy buggers chose the NSO, since all that meant was you had to jog every day and participate in some kind of activity that passed for sports. Earnest, hardworking folk joined the NSS and truly macho chaps (and tough gals) joined the NCC. I believe Ram, as a student, had joined NCC. I would have been totally impressed by this, but somehow I cannot imagine him shooting at anybody or following orders, so I think he must have, somehow, talked his way out of any hard work.
So anyway, that was what we all underwent together and I suppose it created a good sort of bond.... that after 9 years, there was a reunion, which, going by the pictures, looks to have been fairly well attended.
Long intro to what I actually wanted to talk about- which was Mangai's post. Let me get to that in Part II
She's got into the habit of blogging once in a while in Tamil. I've got into the habit of reading, very laboriously, these Tamil blog-posts. Why do I love reading her Tamil blogs? For one thing, it is the type of Tamil I more or less understand, rather than the high falootin', literary type of Tamil in textbooks. Plus, she uses English words once in a while, which I grab on to with the fervor of a novice swimmer being thrown a lifeline while swimming in deep waters.
Anyway, the first post I read is called "Chennai". Lovely! Land of my heart (and pools of my sweat!), how I miss you! I know why she wrote about Chennai. There was a reunion of our batch from the above-mentioned AC Tech on the 15th of August this year and she had attended it. When I say "our batch", I don't just mean our class of 50 from the Biotechnology course. I mean, our batch of more than 200, who belonged to Leather Tech, Textile Tech, Chem Engg and Biotech. We had classes, all 200 of us crammed into one large (and dusty, as previously noted) room together, in our first semester. What were these classes, you ask? How could all these disparate courses have anything in common? Well, you're right. They don't. That's why we took classes in subjects that had nothing to do with any of these subjects, but that were considered mandatory for anybody graduating with an engineering degree. Weird, no?
These core classes were: Engineering Mechanics, Engineering Drawing, Physics, Advanced Mathematics, Technical English, and worst of all, Workshop, which consisted of 1.5 months each of Filing, Welding and Carpentry. Well, to be honest, Workshop was kind of fun. It was the viva-voce examination in Workshop that was truly terrible. I was rather good at filing, welding was a piece of cake- the instructor would come and hold your hand (if you were a girl, that is) and do the welding (he liked holding girls' hands.... we didn't mind, since we could get out of the class quickly. Boys had to wait in line, till we girls finished "welding" and then had to do the stuff by themselves. It was not easy being a girl in Chennai, but there were advantages)- and carpentry was the worst. You had to pick a piece of wood, saw it to the right size, file (or something like that) THAT to make it look neat, and then saw it to make all sorts of joints- T joint is the only one I recall. Anyway, that was not fun. A classmate called Mohammed, God bless him, helped me do all my carpentry- "help" meaning that I would pick my piece of wood and struggle with doing anything with it for the whole hour of the class, then he would come by, and do whatever had to be done with it in 15 minutes and hand it in under my name. Nice of him.
In addition to these classes, we all had to choose one of the following- National Social Service, National Cadet Corps or National Sports Organization- to be a part of, for one year. Most of us lazy buggers chose the NSO, since all that meant was you had to jog every day and participate in some kind of activity that passed for sports. Earnest, hardworking folk joined the NSS and truly macho chaps (and tough gals) joined the NCC. I believe Ram, as a student, had joined NCC. I would have been totally impressed by this, but somehow I cannot imagine him shooting at anybody or following orders, so I think he must have, somehow, talked his way out of any hard work.
So anyway, that was what we all underwent together and I suppose it created a good sort of bond.... that after 9 years, there was a reunion, which, going by the pictures, looks to have been fairly well attended.
Long intro to what I actually wanted to talk about- which was Mangai's post. Let me get to that in Part II
Monday, August 23, 2010
Godawful waste of time
That, in a nutshell, is the movie 'Dostana'.
Why do I watch movies that are
a)at least 3 years old, and b) have already proved to be huge flops
and then curse the movie for wasting my time and then, waste some more time by writing a review on it that nobody will read?
I do not have time for this. I will shut up and head back to lab.
But really man. What a horrible, terrible, awful... wait, let me make this list alphabetical.... awful, atrocious, horrendous, horrible, silly, stupid, terrible movie.
Why did I watch it? WHY???
NO MORE HINDI MOVIES..... until Aamir Khan comes up with his next one. Which, come to think of it, is today.
Hmmm...
Why do I watch movies that are
a)at least 3 years old, and b) have already proved to be huge flops
and then curse the movie for wasting my time and then, waste some more time by writing a review on it that nobody will read?
I do not have time for this. I will shut up and head back to lab.
But really man. What a horrible, terrible, awful... wait, let me make this list alphabetical.... awful, atrocious, horrendous, horrible, silly, stupid, terrible movie.
Why did I watch it? WHY???
NO MORE HINDI MOVIES..... until Aamir Khan comes up with his next one. Which, come to think of it, is today.
Hmmm...
Wednesday, July 14, 2010
Of Feces and the Microbiome
How Microbes Defend and Define Us: http://www.nytimes.com/2010/07/13/science/13micro.html?src=me&ref=general
Boggles the mind, no?
Quick precis of article: Lady has massive, uncontrolled Clostridium difficile infection. Antibiotics don't seem to have an effect. Doctors take a small amount of feces from the husband, mix it up in the saline drip that they have on her and voila! Diarrhea stops, woman recovers. Long discussion on the role of microbes in the human body follows.
Ja wohl?
I do not understand the rationale for this fecal transplant. I mean, if they mixed fecal samples into the saline drip, the bacteria would enter the bloodstream, not the gut. How did she NOT end up with sepsis?
Could her existing C.difficile condition have caused some kind of gut permeability, which then leaked C.difficile into her blood stream, leading to initial inflammation and then an exhaustion of the immune system?
Or could it have something to do with the fact that it is not a single strain of bacteria that is being injected but an immensely complex population of bacterial species, which could somehow detract the body from going into septic shock?
If the underlying rationale was to provide competition to the C.difficile, why didn't they use lactobacillus as a safer option to begin with?
Point to note, appreciate and ponder about: they used her husband's fecal samples. Why do I think this is important? Not because I detect (an admittedly dubious) romantic angle to this business, but because of another point of compatibility. If two people live together and cook and eat together, chances are that their gut flora are similar (or at least, more similar than two randomly selected people). So even if this woman had her gut flora cleaned out by the C.difficile, chances are that her husband's flora might be better "suited" to her.
[Of course, this is a big assumption: for all I know, they may not have been together that long, or perhaps they don't eat together, or perhaps one is a vegetarian and the other, a die hard carnivore. Okay, the last point is not so probable- after all, most times, people marry other people who share their value systems, especially when it comes to food. A hard core vegetarian and a carnivore may live together temporarily, but it cannot be a happy coexistence.]
Coming back to the point, I think it is important that they used someone to whom this woman would have continual, long term exposure to. This is a belief not substantiated by any data.
Technicalities: How did they decide just how much feces to add, I wonder? Was it a one shot bolus, or was it a continual drip? How fresh should the feces have been? How in the world did they mix up a bit of feces to a fine enough suspension that it passed through the tiny needle? Maybe they used a low intensity sonicator?
This is a whole new twist on the Morarji Desai angle. Now somebody should shoot some pee into another person and see what happens. Then, we can vindicate Desai saab's beliefs.
Boggles the mind, no?
Quick precis of article: Lady has massive, uncontrolled Clostridium difficile infection. Antibiotics don't seem to have an effect. Doctors take a small amount of feces from the husband, mix it up in the saline drip that they have on her and voila! Diarrhea stops, woman recovers. Long discussion on the role of microbes in the human body follows.
Ja wohl?
I do not understand the rationale for this fecal transplant. I mean, if they mixed fecal samples into the saline drip, the bacteria would enter the bloodstream, not the gut. How did she NOT end up with sepsis?
Could her existing C.difficile condition have caused some kind of gut permeability, which then leaked C.difficile into her blood stream, leading to initial inflammation and then an exhaustion of the immune system?
Or could it have something to do with the fact that it is not a single strain of bacteria that is being injected but an immensely complex population of bacterial species, which could somehow detract the body from going into septic shock?
If the underlying rationale was to provide competition to the C.difficile, why didn't they use lactobacillus as a safer option to begin with?
Point to note, appreciate and ponder about: they used her husband's fecal samples. Why do I think this is important? Not because I detect (an admittedly dubious) romantic angle to this business, but because of another point of compatibility. If two people live together and cook and eat together, chances are that their gut flora are similar (or at least, more similar than two randomly selected people). So even if this woman had her gut flora cleaned out by the C.difficile, chances are that her husband's flora might be better "suited" to her.
[Of course, this is a big assumption: for all I know, they may not have been together that long, or perhaps they don't eat together, or perhaps one is a vegetarian and the other, a die hard carnivore. Okay, the last point is not so probable- after all, most times, people marry other people who share their value systems, especially when it comes to food. A hard core vegetarian and a carnivore may live together temporarily, but it cannot be a happy coexistence.]
Coming back to the point, I think it is important that they used someone to whom this woman would have continual, long term exposure to. This is a belief not substantiated by any data.
Technicalities: How did they decide just how much feces to add, I wonder? Was it a one shot bolus, or was it a continual drip? How fresh should the feces have been? How in the world did they mix up a bit of feces to a fine enough suspension that it passed through the tiny needle? Maybe they used a low intensity sonicator?
This is a whole new twist on the Morarji Desai angle. Now somebody should shoot some pee into another person and see what happens. Then, we can vindicate Desai saab's beliefs.
Friday, July 9, 2010
A promise
One day, I will live in an apartment that is either
a) On the ground floor with NO steps or
b) Has an elevator.
Am TIRED of climbing 50 steps to my flat every day!
a) On the ground floor with NO steps or
b) Has an elevator.
Am TIRED of climbing 50 steps to my flat every day!
More things
This blog shall be in the form of bullets, because today, I have a neat and orderly mind.
a) I find myself intensely bored with the same old sambar, rasam and boiled veggies, which form my cooking repertoire. These same things were awesome when mom cooked them for me. Now I loathe the very thought of having to cut up radishes for radish kozhambu, I dislike having to make the "vogarNe" with mustard and hing for the rasam and so on.
b) The foods that make me drool right now: a) fettunicini alfredo and b) risotto.
F/A is soooo bland that I cannot understand why I have this hankering for it. Perhaps I only want some cheese. Anyway, both recipes are there on http://thepioneerwoman.com/cooking/ which used to be my number 1 reference for non-Indian recipes. Now, after nearly 12 months of relatively healthy eating, just the amount of butter and cheese that lady uses makes me shudder. It's okay for her- she's on a cattle ranch, no doubt she can work off her fat somehow. It is different for me, when the only exercise I get (or am willing to do) is walk, somewhat slowly, to lab (~2.5miles. Not bad, right?) and that too, only on some days.
c) In effort to make something, ANYthing new, I turned to "Regina's International Vegetarian Favorites", which, when I had bought it some two years ago promised to open up a vast world of new and interesting things to cook. Unfortunately, all her truly interesting recipes require a visit to the grocery store (or many grocery stores). And of course, the only stuff I have readily available are those suited for (bah!) humbug Indian cooking. Anyway, I chanced upon this recipe called "Curried Cauliflower Soup" in her book. It is your normal Gobi sabji, which she then purees.
I should have just made my stupid sabji and eaten it. But no, I went ahead and pureed it and now all I am reminded of is my grandfather. My grandfather, during the year before he died, decided that he was thoroughly bored with chewing food (he later became thoroughly bored of eating itself). During this year, he made the cook puree every single vegetable that she would make for the rest of the family. This way, he would say, he got the nutrition and the taste without the effort.
Curried Cauliflower Soup is depressing. I need to repair it somehow before Ram comes home.
d) I can no longer reliably use the rooting reflex of my baby to check how hungry he is :(
For those not in the know, the rooting reflex in newborns is when you gently stroke the side of their mouth, and if they are hungry, they will open their mouth and root for your finger. Depending on how eagerly Ani would root at a finger, my parents and I could predict how much time we had before he started bawling uncontrollably for his food.
Now, however, he turns towards my finger even when he not hungry, because he wants to chew my finger. I think he is teething, though 11 weeks seems a tad young for that. Nevertheless, he grabs on to anything he can find- his fists, my shoulder, Ram's knuckle etc and chews studiously upon them and makes really loud sucking noises.
Anyway, I guess my little baby is no longer quite as newborn as he was.
e) Ram and I watched "The Judgement at Nuremberg" recently and it is a brilliant movie. I love stories that I can keep recollecting and brooding on for months and months after initially coming across them and this one promises to be in that category.
a) I find myself intensely bored with the same old sambar, rasam and boiled veggies, which form my cooking repertoire. These same things were awesome when mom cooked them for me. Now I loathe the very thought of having to cut up radishes for radish kozhambu, I dislike having to make the "vogarNe" with mustard and hing for the rasam and so on.
b) The foods that make me drool right now: a) fettunicini alfredo and b) risotto.
F/A is soooo bland that I cannot understand why I have this hankering for it. Perhaps I only want some cheese. Anyway, both recipes are there on http://thepioneerwoman.com/cooking/ which used to be my number 1 reference for non-Indian recipes. Now, after nearly 12 months of relatively healthy eating, just the amount of butter and cheese that lady uses makes me shudder. It's okay for her- she's on a cattle ranch, no doubt she can work off her fat somehow. It is different for me, when the only exercise I get (or am willing to do) is walk, somewhat slowly, to lab (~2.5miles. Not bad, right?) and that too, only on some days.
c) In effort to make something, ANYthing new, I turned to "Regina's International Vegetarian Favorites", which, when I had bought it some two years ago promised to open up a vast world of new and interesting things to cook. Unfortunately, all her truly interesting recipes require a visit to the grocery store (or many grocery stores). And of course, the only stuff I have readily available are those suited for (bah!) humbug Indian cooking. Anyway, I chanced upon this recipe called "Curried Cauliflower Soup" in her book. It is your normal Gobi sabji, which she then purees.
I should have just made my stupid sabji and eaten it. But no, I went ahead and pureed it and now all I am reminded of is my grandfather. My grandfather, during the year before he died, decided that he was thoroughly bored with chewing food (he later became thoroughly bored of eating itself). During this year, he made the cook puree every single vegetable that she would make for the rest of the family. This way, he would say, he got the nutrition and the taste without the effort.
Curried Cauliflower Soup is depressing. I need to repair it somehow before Ram comes home.
d) I can no longer reliably use the rooting reflex of my baby to check how hungry he is :(
For those not in the know, the rooting reflex in newborns is when you gently stroke the side of their mouth, and if they are hungry, they will open their mouth and root for your finger. Depending on how eagerly Ani would root at a finger, my parents and I could predict how much time we had before he started bawling uncontrollably for his food.
Now, however, he turns towards my finger even when he not hungry, because he wants to chew my finger. I think he is teething, though 11 weeks seems a tad young for that. Nevertheless, he grabs on to anything he can find- his fists, my shoulder, Ram's knuckle etc and chews studiously upon them and makes really loud sucking noises.
Anyway, I guess my little baby is no longer quite as newborn as he was.
e) Ram and I watched "The Judgement at Nuremberg" recently and it is a brilliant movie. I love stories that I can keep recollecting and brooding on for months and months after initially coming across them and this one promises to be in that category.
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