Gripping Cell

Grown-up stuff

2011-11-04T07:44:00.000-07:00

Wow, it’s been a while since I had a post! It was not that I was too busy to post. I guess I just didn’t get around to it. Also, perhaps having a kid can keep you slightly preoccupied at home :]

I’ve been thinking about ‘grown up stuff’ a bit…you know, getting a job and such. I recently submitted an NIH K99 app this Oct cycle. I initially thought I’ll apply for a tenure-track position next fall. I also want to get a job in a particular region. Turns out that a couple of positions have opened up in schools in the region I prefer…so I’m thinking if I should apply to a couple of places this fall itself to get (i) to see if I’ll get an interview in the first place, (ii) some practice interviewing and (iii) a job, maybe!

One of the issues is…even though the chance of getting the K99 is small, if one does get it, one should not have a TT offer at that time…given that going into a TT position with k99 in hand is better than without it, should I wait and see what happens to the k99 and then apply next fall? It’s not just about money either. The additional training can only help. On the other hand, people say it’s always better to apply early to TT positions. So, I guess I’ll most likely apply to 2 or 3 places this time, which means I should get the research and teaching statements done real soon.

Zzz...

2011-06-07T08:22:00.001-07:00

Auditing with undergrads

2011-05-25T19:57:00.000-07:00

I’m auditing an undergrad class that deals with a topic I’m quite interested in. It is taught by a very good lecturer – apparently, she has won teaching awards every year for 20-odd years. I sometimes wonder what it takes for a lecturer to be a consistent hit among students. I at least know why this particular lecturer is liked by most. Almost everything she says in class is given as a well-written handout. She has 2 different powerpoint slides projected (on separate screens, using separate projectors) *at the same time*. For instance, the left slide is for some main points while the right slide is for examples etc. I think hers is a teaching (and not a research) appointment, and I guess that helps – that way, one can afford to be this elaborate in teaching.

I’m most comfortable just sitting in the last row and being all inconspicuous (I think). Mostly because I feel a bit weird sitting among kids who are like a decade younger. Some of the students bring laptops to class and have it open. I assumed that most of them take notes with it and such. But at any instant I’ve glanced at any screen, I just see either facebook or twitter or some such site. Of course, it’s the student’s choice and all, but I can’t help but think that without the interwebular distraction, there is at least a better chance that they’ll pay attention to the lecturer. But then, there always seems to be a fraction of students who aren’t into the lecture no matter what.

RealiTV...

2011-04-26T19:10:00.001-07:00

Scoopology

2011-03-05T16:47:00.000-08:00

When I was in grad school, I can't recall a single time when I worried about getting scooped. Mostly because we were the only lab studying a particular protein using a particularly esoteric technique. So, the results were unique - we could look at things no one else was looking at. So much so that I didn't even know what the proper meaning of 'scooping' was. I thought it refers to a situation where someone learns what you are about to do and then does (publishes) it before you. It was only much later that I realized that it refers to the act of getting beaten to publishing something, whether or not the competing group knows what you are upto - so, it's competitive but not necessarily malicious.

On thinking about (and getting exposed to the risk of) getting scooped, one thing I realized is that, very often, it is not as bad as it is made out to be. Of course, not getting scooped at all may be ideal...but in reality, lots of people gravitate towards 'hot' topics, and one is bound to have competing groups working on similar problems more often than not. But it turns out that, most likely, different groups have different takes on the same problem. When I was writing my paper (from my postdoc work) several months ago, a paper (in a prominent journal) from another group came out that used a simple but key idea that we had also independently arrived at. But the 'flavors' of our problems and our attacks on them were quite different. The main result was also completely different. Some (well-intentioned) people, who falsely assumed that the key idea we implemented was all that there was to the work, told me that it was a setback for us. Later, it turned out that the reviewers didn't have the slightest concern that someone else had used a similar idea before. They focussed on the way we implemented the idea, what the results were and what it's implications were to the field. It even got accepted in the same journal.

I am no saint and I do have my concerns about getting scooped, but it appears that it is not as much as a setback as it's made out to be. The above does not apply to some studies like, say, publishing the genome of organism x or the mutation that is responsible for some disease. But even in those cases, it's not all or none. One can do a more rigorous analysis of the genome or something else that can make the paper really good, if not 'totally new'. At the end of the day, there is the risk of scooped. One can, may be, avoid people who are 'malicious scoopers' (if at all that is possible). Otherwise, I guess we just get scooped a little, inadvertently scoop a little, and enjoy the science.

Anti-climax...

2011-02-22T22:33:00.000-08:00

Ok, this didn't happen to me - but imagining this scenario cracks me up...

Saturday Afty Experiments

2011-02-12T06:55:00.000-08:00

We all think of 'crazy' experiments we'd like to try 'just for the fun of it'. They are crazy either because the technique is something we are not too familiar with, or the chance of getting a definitive result is pretty slim or simply because we don't know what to expect. The other day, I was reminded of this when reading Andre Geim's interview. He talks of 'Friday evening experiments', wherein he tries things that aren't part of his main line of investigation - things that are fun but unlikely to produce any new data most of the time. As he states it, it takes courage - to just go for it - and long hours - just so you don't take time away from your main projects.
I am not that free-spirited to try things that are too far removed from my main area of study, but I do want to try techniques I've never tried before and phenomenon I've not tried to look at in my main projects. Starting today afternoon. If not every saturday afternoon, atleast every once in a while. If not anything else, I'll atleast learn something.

Robust Measure of Lab Quality

2011-02-04T20:13:00.000-08:00

I heard this gem from a labmate (attributed to her husband):

"You can tell how good a lab is by the quality of printer they have."

True dat!

Baby Boom in ze Lab

2011-01-26T21:41:00.000-08:00

Holy schmoly!

Three postdocs in my lab (or their wives!) are each due to have a kid sometime this year. Turns out I'm one of them.

That's not even the crazy part.

All three babies are due on the same week.

What's that protein doin' here?

2011-01-13T22:09:00.000-08:00

Tee minus one.

2010-12-31T07:52:00.000-08:00

As anyone who saw the documentary '2012' (or was it a movie? anyways...) would know, the coming year is t-1. Some people ask that if the Mayans didn't even forsee their own decline, how can they accurately predict the end of the world. To them I say: is it easier to spot ketchup on your own face or the other guy's face? Yeah, that's what I thought. Need further evidence? Consider 2011. Did you realize that 2+0 = 1+1. Whoa! Start stocking up on Ramen Noodles.

If you think other people are not bracing themselves already, consider this: 99.87%* of students who are beginning graduate programs next month are opting for a 2 year MS over a PhD. (*Obtained from an unscientific poll on a questionable blog such as this. Maybe.)

Lessons from the Poster session

2010-12-19T19:12:00.000-08:00

I like attending the poster session slightly more than talks at big conferences. Mostly because it is a two-way communication. One can toss around ideas and see what someone else thinks of it. When I presented my poster this time, I made the stupid mistake of being present by the poster for only the required duration of 1.5 hrs (every odd numbered poster presenter is required to be present for 1.5 hrs, followed by the even numbered ones for another 1.5 hrs). The reason I bailed out for the other 1.5 hrs was to go see some other posters I was interested in. Pro: I got to talk to those poster presenters. Con: Many people do a single sweep of the posters in the entire 3 hrs, not caring as to which 1.5 hr slot it is in. So, I probably missed out on the interaction with quite a few people who stopped by my poster. I think I had a vague "learning from other posters is more important than talking about your poster for the n'th time" mentality in the back of my mind. Now I think I should have stay put for the full session. Oh well, there is a next time.
One thing I remembered to do was to place my conference ID badge at my chest level by tying a knot atop. Else, the badge was near the belly button level or so. Seemed kind of difficult/odd to spot the names of others who didn't tie it up.

Wassuuup Philly

2010-12-09T21:48:00.000-08:00

I’m not a prolific conference goer. But, as a postdoc, I like the idea of going to 1 or 2 meetings a year. One of the dealios is that the abstract deadlines are supposed to push you to make good progress in your project. My experience is that this does make people work in a more directed manner.

I was at the ASCB meeting last year and I liked it. A few people I know tell me that they always prefer smaller meetings to the big society meetings, but I think that big society meetings have their own charm. I like the fact that there is a lot of variety. I like the challenge of communicating my work to someone who works at the other end of the spectrum.

This weekend, the annual meeting of ASCB is in Philly. I’m told - no, implored - to have a cheesesteak while I’m there. Given that I’ve tried steak maybe twice in my life and didn’t like it too much (sorry, steak lovers), I don’t know if I’ll like this. But I’ll probably try it anyway.

Dear person walking in front of me...

2010-11-27T23:47:00.000-08:00

Thanks for holding that door open, but not always...

Thank you WWW

2010-11-25T08:14:00.000-08:00

The World Wide Web went live on Tim Berners-Lee’s desktop in December 1990. Now, 20 years later, there isn’t a single day we’d go without using websites, be it Google or Wikipedia or what not. For one, my work or personal life wouldn’t be the same without the Web.

While being thankful for such a useful source of information and connectivity, it is also a time to be aware of it’s state as of today. The inventor of the Web warns us in the latest issue of the Scientific American that we cannot take the www in it’s present form for granted anymore. A handful of websites are trying to control our information such that we are not in total control of information we created in the first place. Websites like Facebook, it appears, don’t give a shit about users’ privacy concerns. On occasion, they’ve changed the friggin’ default access options on user data to ‘public’ unless one actively logs in and sets them as ‘private’. They also make it hard to export your information from there to other applications or websites. Certain cable TV companies are also trying to undermine ‘net neutrality’ by proposing to excercise control over how fast you can download things from different websites.

All this calls for proper regulation of the Web. Commercial interests and other nut jobs (“ooh…the government is getting too big”) will continue to create problems, but I hope the Web remains neutral and universal for a long time to come.

Manuscript quality...

2010-11-19T10:26:00.001-08:00

How is your DNA wound up?

2010-11-14T09:51:00.000-08:00

Any reference to the physical organization of the DNA typically brings to mind either the linear sequence of nucleotides (1D primary structure) or the double helix (small scale secondary structure). But how is the DNA in your nucleus arranged in 3D?

The answer to the above typically refers to organization at two different scales: (i) it’s arranged into different chromosomes at the larger scale and (ii) it’s wrapped around histones at the smaller scale. But what about the 3D organization spanning all scales?

Two parts of the DNA that are far apart in linear sequence can still be close enough if the DNA was folded in some way.Recent work that mapped how close each part of the DNA is to every other part (at 1 megabase resolution; all genomic DNA is 3 gigabase) strongly suggests that the DNA is organized as a 'fractal globule'. This arrangement is elegant in that (i) it is a fractal - the same kind of arrangement is present at several length scales and (ii) there are no knots - one can unwind part of the genome (say, for reading it) keeping the rest intact. Another interesting aspect that they discovered was that the gene-rich parts of the DNA and the rest appeared to segregate into two main domains. How exactly this happens remains to be seen. But it seems that the DNA can shift portions of itself that need to be read from the inactive to the active domain depending on need.

Anyway, the next time I think of fractals in nature, snow flakes wouldn't be the only thing that would come to mind.

Are 2 Reviewers enough?

2010-11-10T19:39:00.000-08:00

     I finally got to submit my revised manuscript this week, after a round of additional data analysis and technique validation. Folks who collaborate with me and my advisor on this project are in another continent, so it was email after email back and forth...revision after revision. No complaints though, as long as the paper gets better :).
     We got the initial reviews 2 months ago. Turned out that there were only two reviewers. Why only two? I'm not sure of the reason, but I can think of two possibilities: Either the editor could only find two suitable reviewers at that time, or the editor had enough expertise that only two more opinions were needed in addition to his/her own opinion. Although the journal policy states that the editor would seek the opinion of atleast two experts for the review, I'd presume that three is always considered better. In grad school, I came across an instance where there were again just two reviewers and there was a split verdict. After revision, another reviewer was added to break the tie. Given there were only two reviewers in the first round, is the third reviewer's opinion sought only when there is a split decision or is it sought regardless of the verdict? Or is it not at all unusual to stick with just two reviewers?
     In retrospect, I am kind of thankful that the reviewers raised some points [wasn't too thankful initially ;) ]...it made us look at the problem harder and get at it even more rigorously. Be it two or three, the ball is now in their court. Fingers crossed!

Convincing Argument to Triple Postdoc Salaries...

2010-11-06T07:00:00.000-07:00

Retracted how many papers?!!!!

2010-11-04T20:11:00.000-07:00

Holy shit. I just came to know that, in 2002-03, some guy's 8 Science papers and 7 Nature papers were retracted. I had't even started grad school then. I guess that explains why I don't remember hearing anything about this before. But still. Holy shit.
How come the fraud wasn't detected earlier? Apparently, the fellow was publishing at the rate of a paper every 8 days. So I guess, at that frenetic pace, there wasn't much time for other groups to try enough and be confident of not getting the 'right' result. More importantly, does peer review have the capacity to detect if the data is made up? Turns out that one of the ways they detected the fraud in this case was that there were similar noise levels (presumably dominated by thermal noise) in two experiments at different temperatures. One can easily imagine cases wherein such 'easy' glitches are absent. Then, it appears that the only other way is when other groups try to reproduce the results. This can take months to years. So, it looks like this is the timescale for detecting fraudulent stuff. Peer review appears to be very limited in it's ability to detect fraud, provided there are no apparent gaping holes in it. But I cannot help but think that, in this specific case, atleast some of the reviewers were probably too star-struck to chase after inconsistencies or ask for more controls or what not.

In the Lab on a Halloween Sunday?

2010-10-31T15:22:00.001-07:00

La(m/t)e attempt at anonymity…

2010-10-29T15:52:00.000-07:00

Even though what I post is neither earth-shatteringly important nor shockingly provocative, I have decided to embrace pseudonymity for what it’s worth. Altleast ‘coz it enables more honesty.

Some of you know me in real life, some don’t. It’s all okie, but henceforth I shall post as gc*.

*edited

Troll Face asks...

2010-10-27T20:58:00.001-07:00

The WoW factor!

2010-10-23T23:35:00.000-07:00

According to the International Federation of Journals and Magazines (IFJM), the closely followed yet often criticized impact factor metric is to give way to the newly unveiled WoW factor. In a press release, IFJM president Joe Daplumber said "Every journal and magazine article that appears online will have a 'whoa!' and 'whaa?' button next to it. 'whoa!' meaning 'Whoa! this article just blew my mind!'...'whaa?' meaning 'Whaat? Why on earth would anyone publish this piece of crap?!' The ratio of whoa! to whaa? would be the WoW factor". Daplumber refused to entertain the possibility that there could be reactions other than the above two to any article. He added "anyone can go online and click whichever button they feel like how many ever times they want". Asked if the WoW factor may be subject to the whims of random users, he shot back "whaa? I can't hear you!".

How I landed my Postdoc gig

2010-10-20T20:57:00.000-07:00

There are many ways to look for a postdoc position. Some meet their future postdoc advisor at a conference. One of my friends in grad school asked other PIs in the dept (and related depts) as to who all they think he should apply to, given his interests. Another friend of mine told me that he would only look among BigNamePIs for a postdoc advisor. I know that some, if not most, people line up several interviews and then hit all locations in the span of a week or two. My experience was quite different from any of this.

1) I first emailed one PI who was specializing in a particular experimental methodology. I waited for atleast a week* (don't remember exactly). No reply. Moving on.
*For some reason, I decided to serially (as opposed to parallelly) look for positions. I thought I had some buffer time on hand. Not the smartest thing to do in general.

2) I found my (current) postdoc lab by googling (with my rather broad research field as the search term). The lab was in a different kind of univ (private, smaller student body size), in a different dept and using different methods. Even though the lab was relatively just starting out, I really liked the kind of research the lab was doing.

3) I emailed the PI (my current postdoc advisor) a composite PDF with abstracts of my published/prepping papers and a 'WhyIamAgoodMatchForYourLab' document.

4) PI got back to me after a few days. Went for an interview. End of the day, I met the PI and said that I'd join if the position was offered. Rightaway, the PI said I was in.

Easily, one of the (much) better decisions I've made in my professional life - joining my current lab, that is. I almost want to contact the first PI I emailed to and thank him for not responding to me.

So...what's this all about?

2010-10-16T20:52:00.000-07:00

Lab Hack #2

2010-10-13T20:17:00.000-07:00

It's thursday afty...you're at your bench prepping your sample. You reach out to get a kimwipe but...OhMieGaadz! someone has misplaced it. If this doesn't bother you, you're good to go, but otherwise, here's a simple solution to immobilize your kimwipes:

Actually, I saw a fellow-labbie do this and thought it was quite neat. However, as some of you know, I usually go like this.

Making stuff up.

2010-10-02T11:06:00.000-07:00

I guess it's all relative...

2010-09-28T20:05:00.000-07:00

Can You get it Righto?

2010-09-22T20:57:00.000-07:00

Turns out that our brains suck at estimating conditional probabilities...me and two other labbies were discussing two simple but tricky questions. So I thought I'll post them here and let y'all take a crack at it:

1. There is a couple. One of their two children is a girl. What is the probability that they have two daughters?

2. There is a couple. One of their two children is a girl named Florida. What is the probability that they have two daughters?

Are the answers to the above 2 questions the same? If so (or if not) what is (are) the answer(s)?

PS: If you should know, Florida is a girl name and is quite uncommon these days. Ref: The Drunkard's Walk

Admin Peeps

2010-09-20T21:22:00.000-07:00

Grad School Record and Chance

2010-09-17T20:49:00.000-07:00

Much is said about how one’s performance in grad school determines, to a large extent, where one can end up as a postdoc. Given that letters of recommendation are more often than not positive, the CV of the grad student (# of papers published/submitted) appears to be the primary metric to distinguish candidates.

A simple example (inspired from a book I’m reading now, The Drunkard’s Walk) seems appropriate here. Assume that there is a grad student who’s ability, work ethic etc can all be combined into one quantitative measure: the probability of him/her having a successful year is 0.6…i.e., he/she is more likely to have a successful year than not. I’d say that this is not unreasonable for a ‘reasonably good’ grad student. I think such a way of characterizing a grad student’s chance of success is passable, atleast more so than for postdocs. Postdocs have more control over their success and the postdoc environment is chosen at a time when the person is (academically) more mature. In contrast, the grad student is subject to factors that are much less under his control and together influence his/her chance of success to a greater extent.

Anyway, given a 60% chance of a successful year (however that is defined in his/her lab), it turns out that there is almost a 10% chance that at the end of 5 years the grad student has only one or no successful years. At the other extreme, there is again almost a 10% chance that the grad student has 5 successive successful years in a row. Thus, there is a 10% chance of the same grad student being characterized as an undesirable postdoc candidate and a similar chance as a ‘star’ grad student.

Now, I don’t think potential postdoc advisors are going to look at a grad student’s CV with no papers on it and go “May be he is reasonably good, but is just a victim of random fluctuations”. They have a big pool to choose from and they’d rather go for a candidate with papers to his/her credit. But the situation where cognizance of the effect of chance can help is if the student seems promising in every other way (letters of recommendation, in person conversation etc), except for paucity in the number of papers. Also, perhaps grad students who look back and can’t figure out why they didn’t do as well as they thought they could have(assuming good judgement) can blame it on chance, and start afresh with their postdoc!

Hold that seat!

2010-09-14T22:16:00.000-07:00

One of these days I just might spill some coffee on my seat...

...if I'm stepping away from my seat and I want to hold it for a minute.

Before you blame me for ruining the seat, look here and scroll down to page 8 :]

In vi...what?

2010-09-12T07:38:00.000-07:00

'Data not shown'

2010-09-09T05:25:00.000-07:00

If I had to guess how many of those 'unpublished

observations' see the light of day...

Genomics…me likey

2010-09-07T18:50:00.000-07:00

I usually don’t read biographies…or autobiographies. I am glad, though, that I picked up my first one up a month or so ago. It’s Craig Venter’s account of his life. I would highly recommend it (It kept me happily occupied when in public transit for weeks!).
Irrespective of what some other people told me about him (“he’s supposed to have a big ego” etc), I already liked him for initiating several visionary projects. This book showed that he is not just inspired, but also bold. Venter switched fields and jumped into the sequencing game when he was already an established researcher working on the adrenaline receptor. This was at a time when not even a single free-living organism’s genome was sequenced.
I have worked more with proteins than DNA. Although I did some DNA manipulation in grad school, I always felt like a ‘protein guy’ doing some DNA stuff. I feel that one needs to keep working with DNA (or anything else for that matter!) to become proficient enough. I’ve seen other peeps who do such DNA manipulations almost every other day with ease and had thought that I wasn’t a ‘DNA guy’ – like one cannot work well with both proteins and DNA. After reading Venter’s book, I somehow feel endeared to genomics and gene manipulation. I just started reading a book on the principles of DNA manipulations and genomics, telling myself “it’s never too late” (actually, more like “it’s not that late, I hope. Anyway, it’s friggin’ cool!”).

17 hours of…sitting

2010-08-27T20:04:00.000-07:00

The silver lining? A 3 hour break (at an airport) in between the 17 hours of sitting. I recently tied the knot here, and I’m going to have a ceremony back home. I’ll be there for just over a week. And then 17 hours of sitting again! I’ve had such ‘airplane days’ every once in a while, but my wife (yes, still getting used to calling her that!) has never been on such long flights. So, I guess it’s going to be interesting.

By design, I presume.

2010-08-23T21:25:00.000-07:00

The Dismissive Mindset

2010-08-19T21:44:00.000-07:00

I see it in grad students. I see it in postdocs. I even see it in faculty sometimes. Dismissing other people’s work (such as a journal club paper being discussed) as poor. That may be perfectly ok except that, quite often, there is little reasoning in reaching that conclusion. Some kids do not even bother to read the paper well enough. But they are ready to trash the paper. I have also seen this attitude towards other people’s work/projects. Such an attitude seems all the more quirky when considering the fact that they don’t hold their own work to their 'high standards'. I am all for scrutiny and criticism of papers/research work, but it should be grounded in proper reasoning. Neither in ‘feelings/intuitions’, nor in grumpiness. After all, aren’t we friggin’ scientists?

EDIT: This post was actually triggered by something related in the blogosphere. PZ Myers totally trashed Ray Kurzweil's views on the brain and AI, all the while misrepresenting what Kurzweil actually said.

Fonts.

2010-08-16T18:46:00.000-07:00

Hello Ladies…

2010-08-10T17:10:00.000-07:00

Look at your blog.

Now look at mine.

Now look at your blog.

Now look… at…mine.

Thankfully, your blog isn’t as questionable as mine.

But, if you stopped commenting and being blogrolled, your traffic could be as low as mine.

Look down.

Now back up.

Where are you?

Wherever the heck you were 2 seconds ago.

Does your blog look like mine?

No.

Can it smell like mine?

What a stupid question?!

I’m on a couch.

Muscles inside cells…

2010-08-06T10:17:00.000-07:00

We are all familiar with muscles – specialized tissues that can use chemical energy (basically, the food we eat) to do physical work (eg. running, lifting, chewing). It turns out that there are ‘mini-muscles’ inside almost each of our cells. I am talking about cells as diverse as epithelial cells or fibroblasts or platelets. But to see what these ‘mini-muscles’ are, one has to look at the typical muscle we know a bit closer…I am sure we have all come across the structure of muscle at some point in school/college. Personally, I never cared to remember it – the Z line, H band and all the rest. But, molecularly, the key component is a molecular motor called myosin that uses ATP to pull on actin filaments. This is the event that generates the displacement with sufficient force to power...our moves, if you will. Turns out that there are ~35 classes of myosins and atleast 13 classes are present in humans. The myosin type in muscles is called ‘myosin II’ and is the most well-studied myosin – in fact, it’s called the ‘conventional myosin’ class. Anyway, this molecular motor typically doesn’t function alone, but as a myosin mini-filament, which is a collection of myosin II dimers arranged in a certain way as shown in the accompanying pic. This motor complex pulls on actin filaments on either end. Thousands of them act in concert in a muscle.Now, turns out that myosin II, which is present in muscle, has a few cousins called 'non-muscle myosin II's. As the name implies, the latter ones are present in non-muscle cells. Thus, these ‘mini-muscles’ made of non-muscle myosin II are present in almost all non-muscle cell types. They help cells grip on to stuff …they grip on to neighboring cells and the extra-cellular matrix. Whether they grip on to their surroundings and what they grip on to fundamentally influences what the cells will become (differentiation), how they will grow and what they will do.

Baseball Vs Cricket

2010-07-31T09:52:00.000-07:00

I don't know what is up with these sports-themed posts out of nowhere, but here goes...
I went to my first ever baseball game last week. Till then, I had never even stood and watched a bunch of kids playing softball. So, before the game, a courteous labbie gave me a half hour crash course on the basics of baseball - with a sharpie/window and all. All that I knew till then was that it had vague similarities to cricket. Now, here's my word of advice to cricket-enthusiasts getting to know the basics of baseball (or vice versa): forget what you know about one game when learning the rules of the other, as the similarities are initially a hindrance than a help.
Oh yeah - you run from one base to the next just like in cricket - but wait! - that is not a run yet...it may end up counting for nothing. Hitting the ball out of the park is a home run - but wait! - you still have to run to score your run(s)...I don't know why - mini-victory lap?. Anyways, it is nice to look back after learning the rules and see that there are lots of similarities (which other games use a slab/rod to club a sphere?). The game I went to was very one-sided, so it got boring after 3-4 innings, but I can imagine an even game staying interesting all through.
Inevitably, I was asked "So, how is cricket played?".
I said,"Well, there are three types/formats - a three hour version, a one-day version, a 5-day version."
"A FIVE DAY version?"
"Yup, they play without food or water or any break for 5 days straight."
"????"
Of course, I was kidding. But yes, there is a 5-day version.

Lame PI joke

2010-07-25T09:58:00.000-07:00

When I was on the other side of the planet, I'd have tried shooting hoops may be a handful of times. I, and most of my friends, were much more interested in cricket (still are). Only the richer, more westernized kids played basketball for leisure there. Here, I wasn't sure if I liked basketball all that much. This past two weeks, though, I regularly check out a basketball, go to the court and shoot hoops. Alone. I like this part. No struggling with other peeps over ball possession and such. Even if you are short, you can make up with your skill in making the hoop. The other day, a labbie (labbie, not a labbie) and I were playing this game called PIG (yes, we are lame!)...basically, if you make the hoop from somewhere, the other person has to make it from the same place. If not, you get a P. Then an I. Then a G. At some point in the game, both of us were one miss away from becoming PIGs. Labbie turns to me and says "both of us are PIs!". I go "AAAAAARRGGHH!"

Brett Gelman is hilarious

2010-07-21T23:30:00.000-07:00

Had to post this. Gelman as a creepy 'fan' of Liz Banks...

Mr. Celebrity with Elizabeth Banks from Elizabeth Banks

Bane of the Basement Smoker

2010-07-16T17:27:00.000-07:00

…that’d be nice, if it were only a movie title (not one I’d want to see though).

But unfortunately, this is something I’m having to put up with right now: the people below my new apartment smoke. I’d have no problem if the smell of that smoke didn’t reach my apartment through the vent (but it does)… or if my clothes didn’t start smelling like cigarette smoke…but they do. I’m typically super-adjustable. But I cannot think of just myself, but my s.o too (who is more troubled by this). So, I basically have to get this fixed. I have communicated the problem to the landlord, and I’m told he’d be willing to install some filters in the vents. But I don’t know if that’d solve the problem. Apparently, the people below had already been told previously by my landlord to take the smoke outside. Not good listeners, I presume. I’m thinking of getting an air purifier…have to research as to which kinds can solve my problem. If all else fails, I think I’ll have to move again. Hopefully, the landlord will consent to prematurely end my lease, due to this problem. If he doesn’t, it can be argued using a basic covenant (‘right to quiet enjoyment of premises’) that because the smoke is a health hazard, the lease is effectively broken. I don’t typically argue, so I hope that at least the lease can end amicably if there is no solution to the seeping smoke.

In a related note, I just read that there is no single factor that can screw up your health as much as smoking…including the giant killers (heart disease & cancer ). Just second hand smoke can apparently do considerable damage.

Psychic Octopus and the Silly Media

2010-07-08T23:24:00.000-07:00

Those of you following the football world cup know that Spain edged out Germany in the semifinal. Some of you who browsed the intertubes oflate may also have heard that an octopus ("Paul the psychic octopus!!!!1!") in Germany has been predicting the outcomes of the German games in this world cup correctly. The semifinal loss was also 'predicted' by the cephalopod, breaking the hopes of those who trust magic based on year numbers [images from reddit posts]:

Ofcourse, predicting a win/loss outcome correctly in 5 games just requires a 1/32 chance. This probability may seem small, but if you multiply it by the insane number of 'predictions' read by people based on all kinds of random stuff like the color of dress someone wears to the number of bathroom breaks one takes, any reasonable person will know this can be chalked down to chance.

But hardcore journalists, you see, always go to the 'experts'. The following screencap is from CNN:

. . . . . . . . . . . . . . . . *FACEPALM*. . . . . . . . . . . . . . . . . . . . .

Ah! That looks much better...

2010-06-26T21:17:00.000-07:00

Lab Gripe #3: End-of-day Cell Culture

2010-06-22T21:33:00.000-07:00

You don't do cell culture if something like this hasn't happenned to you...

NIH Diro's LOL...

2010-06-20T22:01:00.000-07:00

Ok, now that I've got your attention...it's not the LOLZ you think it is. This LoL is 'Language of Life', a book on decoding what the human DNA means - especially with regards to personalized medicine. It's written by Francis Collins. I saw him speak at last year's ASCB...he seemed to be a great speaker and had infectious enthusiasm. I usually don't read books (outside of academic books)...I always tend to think "there's so much I don't know in //some subject//, why would I waste time with some other book" (of course, never mind the other 101 ways I waste time!). Somehow, I bought a couple of popular science books recently. The first one I picked is this book by Collins. I was a bit wary initially, considering that his previous book title had the phrase 'evidence for belief' in it. However, this book seems totally about science alone. I am just a few chapters in, at present. It seemed to me initially that his writing was too matter-of-fact in style. But since I care much more about accuracy and insight, rather than great prose, I now actually think this can be a good thing. If reading this book somehow affects how I address/communicate my research problems in some way, I'd consider this time very well spent.

Combo-punch FTW!

2010-06-14T20:55:00.000-07:00

Too little time to throw six punches?

Try this.

Oh nooo...to....thank Gaaadz!

2010-06-05T20:52:00.000-07:00

Last week I learnt that my revised postdoctoral fellowship grant got funded. Phew! I got badly maimed in the first submission (didn't even make the top half!). So, as the results page was loading, I was mentally prepared to miss the cut this time around too...squinting my eyes and imagining that I'll see the word 'Unfunded'. Thankfully, the outcome was different. Looking back, I realize that I did address all concerns raised and at the minimum eliminated any weakness that was pointed out in the first round.

If you count out the 'citizenship-required' ones, as a non-citizen, you can apply for:
(1) a couple of fellowships which basically require you to have had a very productive grad school stint (read here as ~'CNS' pub(s)). Of course, it also looks at other factors (listed in (ii)), but a look at previous successful applicants clearly indicates that unless one meets the above condition, chances of success are very low.
(2) a couple of other fellowships that seem to require 3 factors: (a) a candidate with a promising grad school record (b) good postdoc lab environment (c) good quality proposal [of course!].

Of the three factors, [a] is largely determined by now...maybe one can push for the submission/revision of any remaining grad school stuff, but that's about it. [b] is set once you've started your postdoc. So, [c] is the only thing under one's control. As lessons learnt (with my very limited experience) about what seems to make a fundable proposal, I'd say: (i) choosing a problem people will care about - eg., something that's important and clearly a 'knowledge gap'. (ii) using a very relevant model system (as far as possible). Not going the distance and using an easier, iffy model system may still yield insights, but the reviewer may not care. (iii) collaboration! choosing a collaborator who can contribute in a complementary way to the proposal seems to add much strength to the proposal.

I have to take care of some unforeseen (headache-giving) administrative hurdles (on my end) for the fellowship to kick in. I hope I clear that in a week.

Lab Hack #1

2010-05-22T19:47:00.000-07:00

*Lab hack, as in, anything that makes life in the lab easier/more efficient*

Are your labmates yapping away while you try to write your manuscript? I like all my labbies, but sometimes I have to not listen to people talk...especially when I'm trying to read/write something. My supervisor suggested I use headphones. I tried using them without music - but my ears are still trying to still listen to people...I tried to listen to music - but then, I listen to music and am unable to concentrate. HMMPGH!!

Recently, Rainymood has come to my rescue...I listen to the rain building up in the background, phase out of the lab, and phase in to whats on my monitor. It just might work for you too...just don't be disappointed that it isn't really raining when you take your headphones off!

Out of state

2010-05-15T03:03:00.000-07:00

I'm going slightly out of the state for a few days. Told my labmates that. They said something about cheesehead hats. I asked them why anyone would make a hat out of cheese. Hilarity ensued. Had NO idea it was related to football.

Yippee!

2010-05-11T21:48:00.000-07:00

This is off-topic for sure, but this is great news from Bulgaria... Viswanathan Anand, playing with black pieces, retained the World Chess Championship title after defeating Topalov in the last game. With all the extraneous stuff - Anand having to travel 40 hrs on the road to get to Sofia in time (due to the Icelandic ash), Topalov citing obscure rules to enforce no communication between the players during all 12 games etc - this was a fitting end to the match.
A dozen years ago or so, I saw him (he was famous then too) standing in front of his house (which was on the same road as my high school)... I should have gone up to him to get his autograph!

Best. Book. Ever.

2010-05-08T10:46:00.001-07:00

Preprints, anyone?

2010-05-04T23:08:00.000-07:00

I’ve been wondering about how common it is for people in the (broad) biomed field to actually upload their not-yet-peer-reviewed manuscripts (i.e., preprints) to a preprint server such as Nature Precedings. I think it is fairly common for people doing physics to upload their preprint on arXiv. However, I personally don’t know anyone in biosciences who mentioned to me that they have their manuscript up on Precedings or any other such server (if it exists).
I do not know if people in biosciences simply don’t find much use for a preprint server or if the concern on getting scooped is a factor. My mentor tries to be quite open about the science in the lab without much inhibition. I think I have caught on some of that goodness. I had a meeting poster of mine out on f1000. But I am not really concerned that its out. Also, there are positives to exposure too. Anyway, I guess one has to draw a line for oneself on when to put one's research out. I don’t like being too closed, but I guess prematurely talking about some stuff may not be ideal either.

That is it!

2010-05-02T14:18:00.000-07:00

I've never been more attracted to the earth. Literally - with a force 890 N. Yup, I have attained the dubious distinction of reaching 200 lbs.
My 1st year of postdoc life has been good in several ways - the work environment is excellent (including kind & amazing supervisor) and I work on a project I love. Personally, I've been quite happy. However, I've not been intelligent enough in taking care of myself. I was 170 odd lbs when I started my postdoc. That's ~+30 lbs in just over a year. That is it, I say!
In the words of my favorite super-villain (read it like him for effect:)...

“So…about your Marriage…”

2010-04-29T21:34:00.000-07:00

Where I grew up (on the other side of the planet), it is not common to be that much over 30 and not be married. When one goes home for vacation, inevitably, the topic crops up. Usually brought up by the slightly more conservative parent:

“So, family friend/colleague XYZ asked about you…and your plans for marriage…”

Me: “Who’s XYZ?”

“He is…doesn’t matter…so, anyway, what have you decided?”

Me: “I will let you know when I decide”

“But that’s what you said last vacation”

Me: “Hm…yeah”

“XYZ mentioned that JKL’s daughter just finished her studies…”

[Me thinking: OMG---HOOK-UP-ATTEMPT---ABORT-CONVERSATION---ESCAPE]

Me: “No, wait, I’ll tell what I’m going to do next time I come”

Actually, my parents are quite understanding of me, but such mild pressure to get married is not uncommon back at home. Now, I do have to say that I do not look down on parents-hooking-you-up-with-family-friend type stuff. I’m not really into it, but it’s just one of the ways for some people to meet people. I also understand that parents usually have only good intentions…but you can’t really get married unless you want to (for whatever reason). I just think that one should do what one wants to – get married at 20 or 40, or not, whatever works.

In Nippon?!

2010-04-27T19:27:00.000-07:00

Turns out that in Japan there is discrimination on the basis of....wait for it...blood group!

According to a BBC News report, interest on blood types and how it affects personality types is widespread in Japan. It is beleived that:

Blood group - Personality type
A - Dependable and self-sacrificing, but reserved
O - Decisive and confident
AB - Well-balanced, logical, but distant
B - Flamboyant free thinkers, but selfish
Apparently, people with the B blood group are disadvantaged in the dating scene and in job interviews, as they are seen as being disorganized.

It's surprising to me that such superstitious stuff can survive in such a techno-savvy society.
What blood group am I? Lets just say I'm not moving to Japan anytime soon.

Physicist in Biologist's clothing

2010-04-22T21:00:00.000-07:00

How can you tell when a physicist is writing a bio paper?

The first freakin' reference cited is Alberts et. al.'s Molecular Biology of the Cell.

Down time

2010-04-17T12:20:00.000-07:00

You know there is a problem when...

'Talking science' included for contrast with 'talking shit'.

Experimento Clásico

2010-04-14T16:57:00.000-07:00

Turns out that rather than the primary tumor itself, cancer mostly kills people when cells from the primary tumor migrate away and cause secondary tumors at other sites (called metastasis). E-cadherin, which is one of the main cell adhesion molecules (CAMs) on cells that mediate adhesion to neighboring cells, is usually lower in levels as cancer cells escape from primary tumors.

I came across this paper from 1944 (D R Coman, “Decreased mutual adhesiveness, a property of cells from squamous cell carcinomas”, Cancer Research, 4, 625) wherein Coman pulls apart pairs of normal or cancer cells and shows that the force required to separate cancer cells is significantly lower.

The 2 most interesting things about the paper that caught my eye were (i) the physical, quantitative approach - forces were quantified by measuring the bending of the needles as the cells were pulled apart (these days, we measure how much an AFM cantilever bends); (ii) the thought that this adhesiveness may be important. Remember, this was done several decades before people even knew that CAMs existed.

Given the tendency for most authors (including me?) to cite almost no papers that are older than a decade or two, I wonder if something is being missed by not referring to many of the original articles and the rather bold ideas in them.

How to Read Papers

2010-04-10T17:09:00.000-07:00

These days, I am parsing through quite a few papers since I am writing part of a review. It seems like you can actually read more than meets the eye with some of the words people use...

“… is largely unknown.” - our paper is exactly about this.
“Interestingly,…” - We don’t have a clue why this happenned, but here you go.
“We found that … is consistent with literature.” - This is known, but we are going to include it in our paper anyway.
“Surprisingly…” - We were predictable last paragraph just to shock you with the following.
“This is a novel...” - Atleast, no one did this before.
“We proceeded to…” - We just happened to try this out next.

... and so on, but you get the drift. Of course, many papers are solid and the wording is appropriate, but it is fun to spot these sorts of wordings in other papers.

Release the Kraken!

2010-04-06T19:46:00.000-07:00

Lab Gripe #2: pH-ing woes

2010-03-31T22:52:00.001-07:00

Ctrl-C...Ctrl-V...tweak

2010-03-27T14:02:00.000-07:00

If one looks at the structure (or sequence) of cell adhesion molecules (CAMs) and extra-cellular matrix (ECM) components, one finds that they are most often modular in nature. That is, they are made of parts that have distinct functions (although sometimes the parts also do some functions together). Not only are they modular, the modules that make each protein are also drawn from a global, common set of modules. Just like you can build either a house or a fence with lego blocks, you can build distinct ECM molecules or cell adhesion molecules starting with a common set of domains.

How did this happen? Gene duplication and divergence – that is...ctrl-C, ctrl-V, tweak. An ancestral gene coding for one module gets duplicated first. One of the copies is now free to change, randomly searching for new function. While the fold (overall topology of the module) is usually conserved, the residues (amino acids that make up the protein) can change by genetic mutations, leading to modified function. Different gene copies may also get pasted next to one another in which case they may form a new multi-modular protein. This is not only evident in CAMs, but also in all other kinds of proteins. Hence, the number of proteins we have (of order 10,000) exceeds the number of protein families by an order of magnitude.

Spring Break

2010-03-20T10:35:00.000-07:00

What's in a (blog) name?

2010-03-18T23:16:00.000-07:00

Feynman said that if there is one piece of info that conveys the most about our scientific knowledge, its that everything is made of atoms.
Now, if there is an almost parallel statement to be made about biology, it ought to be that the cell is the fundamental unit of life. (yes, yes, I do see that biology is a subset of science and that cells are made of atoms...but we are a long way from simulating an entire cell!)

Given that it is the basic unit, there are a lot of things the cell does - like eating, destroying (~phagocytosis), burning (metabolic reactions), barfing (~exocytosis), dying (apoptosis, necrosis) etc. Now that brings me to my favorite thing it does...gripping. It uses transmembrane proteins such as integrins and cadherins (among several other proteins or even carbohydrates) to not only stick to (adhesion) but also pull on its microenvironment.

Whats with all this pulling? It's important for atleast two reasons: Those forces shape cellular level morphologies. But they also change the cell itself by inducing biochemical signaling. And as anyone who has seen entire signaling pathways will tell you - they look so complex, they could be life itself.

Lab Gripe #1

2010-03-14T12:13:00.001-07:00

How much do Asst Profs make?

2010-03-03T18:09:00.000-08:00

As someone who might end up in academia, I sometimes wonder how much money an assistant professor makes these days. In the place in which I am a postdoc now, I know that the assistant professor salary is ~$90,000. But this is definitely on the higher end.
FemaleScienceProfessor has an interesting post up in which she asks her readers to answer the same question. The results indicate that its reasonable to expect that you would earn $65,000 a year when you start off. Considering that the median household income for 2008 is ~$52,000, it is not a bad salary by any stretch. However, it does not seem to match what several people I've talked to fancy as good.

This is how we do it...

2010-02-27T11:47:00.000-08:00

I thought I'd share the following video of a 'road-side restaurant' in the state where I grew up. Usually, these 'restaurants' offer decent food for a cheap price...ideal for people who engage in physical labor all day but do not earn much. However, it'd be better if you have a well-prepared immune system if you are going to try one of these places. Here, these hard-core cooks show what we are capable of with a little practice...

Cadherins FTW!!1!!

2010-02-15T01:27:00.000-08:00

Oh, hi!

2010-01-27T21:03:00.000-08:00

Me loves Intro courses!

2010-01-10T20:04:00.000-08:00

As a postdoc, doing research, reading papers and writing/presenting is supposed to take up most of your time. Somewhere in this medley, learning new subjects ought to find a place. I hear some say, "At this stage, you should be able to read a book for whatever you want to learn". I, however, have always been a fan of sitting in the class - sitting and listening to someone who tells you want you need to know and organizes the info appropriately.
I wanted to take a course that's an intro to a particular disease. There was one undergrad intro course and another grad 'molecular mechanisms' course. In spite of well-intentioned advice from an undergrad in my lab that the undergrad intro course may be too low-level and uninteresting, I chose to audit the former. I usually take sometime to warm up to new subjects, so I thought this was worth a try. I just attended one week of classes so far, but it looks good and I hope it has all I expect from good intro to a subject:
- historical perspective, esp. the non-linear evolution of ideas
- specifying what any new term means as it arises, instead of having 10 new terms in one sentence to bedazzle peeps
- bird's eye view of mechanisms instead of spending half an hour with the crystal structure of a protein telling which residues move how
- overall current level of understanding of things

Integrin (a.k.a SuperStarzz!!!!!1!11!!!)

2009-12-25T22:30:00.000-08:00

Roughly speaking, the 'sort-of-solid' parts of our body (excluding blood plasma etc.) consist of 2 components: the all-important cells and the so-called extra-cellular matrix (ECM). Cell adhesion molecules (CAMs) are cell surface proteins that make cells stick to neighbouring cells or to the ECM.

If I have to pick one molecule as the star of the cell adhesion field, it has to be Integrin. It is the primary CAM cells use to stick to the ECM. Integrin is a heterodimer - i.e., it has two subunits, alpha and beta, each of which is a polypeptide chain. The subunits are bound to each other by non-covalent bonds. It is also a transmembrane protein, like almost all other CAMs.

There are 24 types of alpha sub-units and 9 types of beta sub-units. Only certain types pair up, leading to well over 20 integrins in mammals (instead of over 200 if alpha and beta types pair up exhaustively). Integrins mainly bind to ECM components such as fibronectin, laminin and collagen. However, some integrins, such as the ones that have the beta-2 subunit, bind to CAMs (such as ICAM) on other types of cells. We shall get friendly with most of these proteins in the posts to come.

If James Cameron was a P.I....

2009-12-17T23:57:00.000-08:00

Here's a quote from an interview given by James Cameron (director of Titanic, Avatar) recently:

"It's very helpful when you try to do something radical and new, like "Avatar." When I pitched it at Fox, it was good to have a track record of successful films, to be able to say to them that I've never directed a film that has lost money, and I'm not about to start now. That was maybe the most compelling thing I said when I was asking them to fund a very expensive film in which the main characters were going to be completely CGI, with blue faces and big golden eyes and tails! Sometimes they'd ask, "Do they need to have tails?" Like it was about the tails. Well, it wasn't about the tails, it was about the fact that they were computer-generated characters and their unease with that. But I had this track record, which helped. I don't care how good the script was, I could not have gotten "Avatar" funded if I hadn't made "Titanic"."

He almost sounds like a principal investigator on a grant:
Avatar <--> Risky new project
Fox <--> Your favorite funding agency
very expensive film <--> Big-budget project
CGI <--> Costly, time-consuming experiments
"Do they need to have tails?"<--> 'Do you need to buy that confocal?!'
Titanic <--> prev. published CNS paper

My first ASCB meetingianzo!!

2009-12-12T19:37:00.000-08:00

I attended a major cell biology conference for the first time, this past week (my previous ones were either biophysical or a focussed meeting). I presented a poster about my work on cell adhesion. I was fielding questions and briefing visitors at my poster for ~ 3 hrs, even though I was supposed to be there only for 1.5 hrs. No complaints, though, as it was thoroughly enjoyable.

My favourite talk in the meeting was one from Keith Burridge's lab at UNC. It was about signaling molecules called Rho GTPases and their regulation by other related signaling molecules.

Which reminds me...I initially thought I shall introduce cell adhesion related topics/molecules/mechanisms in this blog in a more or less linear fashion, going from the already-introduced to the next-in-line. However, I think I shall switch now on, to a more haphazard-yet-tractable style - i.e., I shall take the liberty to mention and discuss about molecules here-and-there, the hope being that an occasional visitor (to the blog) would be able to learn about the molecule/mechanism in that post, but fitting that pocket of info/understanding into the 'big picture' of the cell adhesion field may be left to occur over time...by reading many posts or by reading some other material somewhere else. I would hope that this would be ok.

Our molecular glues...

2009-11-14T15:57:00.000-08:00

Cell adhesion molecules (CAMs) are proteins* that are present on the surface of all of our cells and that due to their sticky nature make our cells sticky.

Many different CAMs are present in our body. They are typically embedded in the lipid bilayer of the cells. They have an extra-cellular portion which is the sticky part, a trans-membrane portion which is the part embedded in the lipid bilayer and an intra-cellular portion that can in turn bind to or regulate other proteins inside the cell.

“CAMs are sticky alright…but what do they stick to?” I hear you say. They stick to CAMs on the neighbouring cell or to other proteins present in matrix-like material outside cells (called extra-cellular matrix). Some CAMs even bind to non-protein molecules like sugars. All this will become clear when we discuss the different types of CAMs.

*(In case you are not familiar, proteins are polymers of small molecules called amino acids. Proteins are the nano-machines [size ~10 nm] in us that do most of the sub-microscopic level chores in our body – all those chores going on that make us living organisms rather than a lump of organic matter)