arnabocean

— by Arnab Gupta

Music: lyrics for Khnoro Amar Fossil, from Fossils 4

November 10, 2013

The Bangla Band Fossils came out with their new album Fossils 4 recently, and I’ve been listening to it frequently. Unfortunately, I can’t seem to find the lyrics of some of the songs anywhere online, so I transcribed some of them myself. Here’s one. :)

Listen to the album on Saavn or Dhingana. (Fossils band members, and Rupam Islam in particular—why not launch the album on iTunes? Makes obtaining music easier for people away from the country.)

Matlab: find a string within a cell array of strings

October 14, 2013

I just wanted to jot down a few points about Matlab programming. Specifically, this is about finding a string within another cell array of strings, where the thing I’m really interested in is the index of the cell array where the reference string occurs. For example, if my reference string is 'Gamma', and my cell array is {'Alpha','Beta','Gamma','Delta'}, then the result of the code should be 3.

More on the Naked Mole Rat

October 12, 2013

I’ve written about the naked mole rat before, about how it seems to be immune to acid.

Well, it turns out it has more tricks up its genetic sleeve.

To compare how the naked mole rat made their proteins, they inserted an engineered gene in the naked mole rat as well as in mice, which allowed them to compare the rate of errors in making proteins. And here’s what they found:

[The naked mole rat] built the engineered protein far more accurately, in other words. Naked mole rats, the scientists found, made anywhere from four to ten times fewer mistakes. Yet the naked mole rats can make their proteins as quickly as the sloppier mice.

This seems to be a fascinating creature the more we study it!

I wonder, though, why other species did not pick up this brilliant piece of evolution. Are there side effects to this that are detrimental, overall, to other species but which don’t affect the naked mole rat? As I said in my earlier post, intriguing.

(Original source, quoted by National Geographic: Jorge Azpurua et al.“Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage.” PNAS 2013

Dissertation Proposal

July 16, 2013

I defended my dissertation proposal today.

What this means is that I now have an approved (by my dissertation advisory committee) framework for the research that will grant me my Ph.D.

There were no bad surprises that caught me or my adviser off guard. My advisory committee members are really great people, and we were able to discuss what I’m proposing to do very well. They suggested a couple of things, but they were ideas that me and my advisor had been discussing ourselves only recently, so even that wasn’t out of the blue for us. Although—to an extent we were, or at least I was, thinking of doing those things for different reasons than what the committee suggested. That’s the thing with these defenses—you get a different perspective on what you look at everyday.

Well, one more step completed. This was on the calendar for quite a long time, and it’s nice to get this done. :)

On the other hand, this is the beginnning of the next, arduous path—now that I’ve proposed something, I’ve to actually go ahead and do those things! Lots of experiments to do; many lines of MATLAB code to write and debug—fun times are ahead!

But for now—a bit of a break. Well earned, if I do say so myself. :)

My scientific writing workflow

June 30, 2013

I am not fond of MS-Word. Correction: I cannot really tolerate MS-Word, and the only times I really use it are for work, where documents must be shared, modified, commented upon, and tracked for changes between multiple authors, contributors and edit cycles. For those particular circumstances there really isn’t another viable alternative to MS-Word, is there.

But of course, the criteria for my own scientific writing are very different. The only sharing and discussion is with my dissertation adviser, and I can easily handle one other contributor without needing MS-Word. So, of course, I’ve moved as far away from that bloated, cranky piece of software as I can—which is to say, completely away.

Instead, here’s what I use.

On using (or abusing) bio-technology

June 24, 2013

I wrote a small piece on fair use of our biotechnology on my Tumblr, but since I’m planning to write longer pieces on this blog, I wanted to cross-post it here as well.

Joe Hanson, of It’s Okay To Be Smart, wrote:

Can Biotechnology and Genetic Engineering Save an American Icon?

What I find so interesting is that the techniques being used to save this tree, and one day reintroduce it to the wild, are not that different from those that are used to create genetically modified crops. How does saving a dying species by inserting a gene differ from creating an herbicide-resistant soybean, or rice that produces extra vitamins? I have my opinions, but I want to know: What do you think?

My thoughts are below.