Monday, January 6, 2014

Weather insanity


Did you see what it "Feels like" Right Now?? -11F! And that, rest of the world which follows a saner temperature scale, is  -24 C!

I have just came back from outside after a 10 minute scurry, collar raised up, neck muffled, head (unfortunately) inadequately covered, gloved hand clutching on to samples and culture plates, nose watering, eyes burning and cheeks hurting.

Note to self: take day off from work tomorrow, where the high temperature (high, mind you... not some random point in the day, but high) is 8F, with wind chills approaching -25F.


Why am I in this country again?

Friday, December 13, 2013

The Superstition of Scientists

Perhaps it's the fact that many procedures in molecular biology are seemingly persnickety: the wrong pH, the wrong temperature, the wrong way of agitating a solution can throw an experiment completely off and can take a scientist ages to figure out what went wrong. Mol Bio is something like Potions, in Harry Potter: if you stir a pot 5 times clockwise, instead of anti-clockwise, under a half moon, instead of a full moon, you are bound to turn yourself into a frog.

Experimental molecular biologists spend ages optimizing protocols and are notoriously conservative about change: nobody follows "if it works, don't fix it" as a molecular biologist. A protocol might take 8 hours, but a mol biologist won't approach a quicker protocol without many mental palpitations, prayers, qualms and shudders. And even after trying the quicker method, he/she may well shrug and say, "My old method was better. It might take me a day and a half of incessant labor, but I think the yield and the quality were better"

Thus, if such a person were to use a premade kit and got beautiful results, well... this person will be unlikely to use any another product for that purpose.

This is the mentality that companies selling molecular biology products take full advantage of. Check out Qiagen's whole genome amplification kit: they have one for genomic DNA, one for frozen tissue and one for single cells; each one more expensive than the previous. But the underlying principle of amplification is exactly the same.
When you check out their protocol for each of these kits, the components are named different in order to make a consumer feel like they are paying (an arm and a leg) for something secretive and magic that will instantly provide them with the answers they seek.

For example, take Table 5 of the Repli-G Single Cell Handbook "Preparation of the master mix"
Component:
H2O sc
Repli-g sc Reaction Buffer
Repli-g sc DNA Polymerase

Now take Table 3 of the Repli-G MiniMidi Handbook "Preparation of the master mix"
Component:
Nuclease free water
Repli-g Mini Reaction Buffer
Repli-g Mini DNA Polymerase.

They are exactly the same components, being marketed under different names. But can you use the Repli-g Mini kit (cost for 25 reactions $199)  for a single cell amplification, instead of the Single Cell kit (cost for 24 reactions $488) ? No! Because they have tested the Single Cell kit on single cells and they know that it works. If you were to use the cheaper kit, for this application for which it is not suited, they cannot guarantee that you would get consistent and reliable results.

The hapless lab tech/ grad student/ postdoc convinces the PI that the money must be spent, and the expensive kit is bought, which probably works beautifully and now, this person will continue to buy the more expensive kit and will never try out the cheaper kit because of the suggestion that it might not work.

Shoot. Gotta stop before I am ready. And when I come back, I'd have forgotten the original point of this post....


Thursday, November 21, 2013

The Silly New Fad in Scientific Paper Publishing




What's this new fad of putting up the picture of the lead author in scientific publications?

It's useless and distracting. I glance at the paper and instead of focusing on the title, my eye is caught by this picture... and I wonder how she can see with hair falling across her eyes, if she's outdoors trekking somewhere, if this picture was recent, how much this lady can trek, whether she had this picture taken specifically for this paper, and if so, why did she choose this particular picture, and if I don't have something better to do than wonder about random people.


Please, publishers, don't waste the 3-5 minutes of my attention that you've grabbed. Just tell me the main scientific story and store the biography for a news release. That same space could have better used by putting a little box with the highlights of the paper.




Wednesday, November 13, 2013

Kids, Language and Accents

Ani has a friend, L, in preschool.

L's parents speak Tamil to her, insist on her answering in Tamil and speak Tamil to each other.

I speak Tamil to Ani, but it is peppered with English. English is the language with which RK, Ani and I converse.

Ani speaks English with a strong Indian accent at home (complete with the head bobs... I didn't realize that either RK or I did that until Ani started doing it) and English with a strong American accent at preschool. He understands Tamil but he doesn't think in it. On the other hand, L speaks English only with an American accent, but Tamil with a Tamil accent.

Even more interesting: L calls Ani the way his name is supposed to be pronounced: A-nee
However, when she refers to him in the third person, he becomes 'Aah-nee', the American-accented version of his name.

It's one thing to read about kids unconsciously absorbing the culture around them, quite another to see it in real life.



Tuesday, October 29, 2013

Quote on attitude

“The longer I love, the more I realize the impact of attitude on life. Attitude, to me, is more important than facts. It is more important than the past, than education, than money, than circumstances, than failures, than successes, than what other people think or say or do. It is more important than appearance, giftedness or skill. It will make or break a company...a church....a home. The remarkable thing is we have a choice every day regarding the attitude we will embrace for that day. We cannot change our past...we cannot change the fact that people will act in a certain way. We cannot change the inevitable. The only thing we can do is play on the one string we have, and that is our attitude...I am convinced that life is 10% what happens to me and 90% how I react to it. And so it is with you...we are in charge of our attitudes.” 
― Charles R. Swindoll



Guess where I heard this? In a public bus in Boston!

Have been so inspired by this that I've resolved to maintaining a good attitude at all times.

And so far it's been 5 days (and counting)!


(kind of slipped up last night when I hissed at Ani harshly enough to upset him.... he kept trying to twist Durga's hand so he could hold it while going to sleep, making her wake up and cry, and making me want to rip my hair out)

Other fantastic news:
a) ASHG 2013! (See prev blog post for scant details)
b) Acadia/Boston! (yes, we were there. Beautiful and fun, both places. I'm so glad to be back home, though)
c) Figured out how to get average promoter methylations while controlling for CpG island presence!
(...aaand I just lost my audience with just that one sentence)

Tuesday, October 22, 2013

Notes from the ASHG 2013

My first gigantic conference! Used to attend Keystone as a grad student. Am at the American Society of Human Genetics annual conference in Boston this week and the scale of this is greater than anything I've attended before. Nearly 7000 attendees!

Currently at an exhibit hall which is the size of a football field, waiting for the President's speech.
In front of me is a Japanese group, all of whom bowed to each other multiple times. I imagine them saying "After you, dear chap" "No no, after you!" after each bow.
Multiple attempts to figure out who should sit down first.
10 minutes later: okay, they've figured it out. Now they've whipped out their cameras and are taking pictures of each other.
5 minutes later: they are now taking pictures with some of the award winners.
Update: oh wait! It's not an award winner who's posing for pics- it's the president!

Am sitting waay in the front- 4th row from the stage. I figure I should get my money's worth of education. No snoozing while at the conference! There are zillions of rows- there's supposed to be a screen every 25-30 rows, and I count 3. There are about 75 columns.



Monday, September 16, 2013

My article at the Family Medicine journal

http://www.stfm.org/fmhub/fm2013/September/Varsha582.pdf

Hurray!

What does it say about me when my sole first-author article in an academic journal is a creative writing piece, rather than a scholarly piece that advances science?

Note to self: Must publish PhD work. Soon! Aaarrggh!