Good question. I first thought about writing on my personal blog about atheism a while ago when I read the blog of a high school student in the US who was being persecuted at school for being atheist. I can’t for the life of me find that blog and all I remember is that it was hosted at blogspot.com and that he was using that ugly yellowish-polka-dot theme.

But if you meant why am I an atheist. Well, that requires a longer answer and one that a single blogpost would not suffice. Simply put though, atheism makes sense. If you’re of a scientific bent of mind and you honestly think about things, there really isn’t any reason to posit the existance of gods.

Maybe more in future posts… 🙂 Welcome!

Time to gloat…

… for a little while at least! 😉

I’ve been an enthusiastic (and decent) quizzer for most of my college years in Bangalore. Ever since I moved to Bombay, I’ve not had much chance to take part in any quizzes until the Bombay Quiz Club came around.

They’re a group of quizzers that coalesced to do some informal quizzing every so often in Bombay. One thing led to another and they now have a mostly fixed schedule of meeting every two weeks for some intensive quizzing and recently they’ve even decided to formalise the organisation.

But even though they’re more than a year old, I never got around to attending a quiz until about a month ago. It was a lot of fun and the team I was in placed second with me answering a few questions. I attended the next quiz, two weeks later and once again the team I was in placed second, but this time only because the cricket geeks in my team hammered away at the round of 20 cricket questions rocketing up our team from 5th place to 2nd!

And then this week, this happened. So for a short period, I’m the “top quizzer” in Bombay! 😛 This won’t last, of course, unless I’m really lucky through the year and always end up in winning or placing teams.

The State of Evolution

Kansas Evolution

From the cartoons of R J Matson

Welcome back!

If you’ve been following us at the Blogspot blog, its great to see you here! While we’re still sort of working out how this blog is going to shape up here (including a name change possibly), the content is not going to change.

I guess a science blog will fit right in at a site called Absolute Geeky! What’s the story behind that name? Well, I’d long wanted my own domain and when I finally decided to go ahead and book it, I decided my geekiness is what sets me apart from most people. So I didn’t have to spend too much time figuring out what should be called (and thanks to A for the suggestion.)

Expect to see some new posts here real soon now since I’ve berated Madgenius and Samudrika for not posting, they’ve both assured me that they have new posts up their sleeve.

Going google-eyed over AI

It all started with this blog post by John Battelle which mentioned Larry Page talking about AI at an AAAS conference.

Who wouldn’t be interested? Harish and I watched the short clip on ZDnet and we were both a bit taken aback by what Page was saying. (You can get a video of the complete speech on this page.)

If you look at your DNA its just about 600 MB compressed, which is smaller than any operating system. Your Linux, windows, any operating system. That includes booting up your brain, right … by definition. So your algorithms are probably not that complicated, its probably about the overall computation.

I spotted the obvious flaw there that genome size is directly related to complexity of the system. Now any biologist worth her salt will tell you that this is simply not true. Gone are the days when we believed that knowing the complete genetic code of an organism will tell us everything we need to know about that organism. Far from it, the questions raised by sequencing genomes are far more than ones it answers!

But what does this all have to do with artificial intelligence or AI? Well apparently, a lot of people are buying Larry Page’s argument! Now believe what you will about the complexity or simplicity of AI. I’m no expert in the field. But to use the supposed “simplicity” of the DNA “program” to prove your point about AI is plain wrong.

I spent some time explaining to Harish the biology behind my thinking and he converted his understanding into a blog post with a clever title. He also went around posting comments in the blogosphere talking about why Page’s logic was flawed and pointed back to his post. Except for a couple of people, most didn’t understand the point Harish was trying to make with all the biology in his post, so let me try it this one time.

Page’s argument as I understand it is:

  1. Human DNA is simple to understand.
  2. Human DNA programs for the human brain.
  3. The human brain makes human beings intelligent.
  4. Therefore, AI is simple

All cut and dried. What’s wrong? Well, a couple of things. I could debate about how simple or not simple human DNA is, but lets assume it is simple. We’d still be stuck at step 2. DNA does NOT “program” in any sense the human body or brain. Using the metaphor of a “program” is quite wrong and it is this precisely that which leads most people to make mistakes in assuming what DNA can or can’t do.

My point is that the sequence of DNA in a genome is an incomplete description of a living system. Therefore it is not a good way to estimate how easy or hard it would be to build an AI system.

I do not know enough about AIs, nor the current state of research in that field to be able to debate how close or far away we are from building one. But I do know enough biology to tell you that using DNA to argue that AI is around the corner is wrong.

The Diet Coke and Mentos Experiments


Now if only science experiments in schools and colleges were like this!

What a great way to learn about the contents of carbonated beverages, a common candy, materials science (the surface of the Mentos), theories about boiling, phase transitions, nucleation sites… and more!

(If you’re too lazy to wait for the video to download and watch it, it’s these two guys from eepybird.com who have made very elaborate fountains using Diet Coke and Mentos. Put a Mentos into a two litre bottle of Diet Coke and voila, instant fountain. Of course, it’s more complicated than that, but still relatively simple. Watch the video, it’s a lot of fun! And well choreographed!)

Stranger than fiction

Sometimes science can be stranger than fiction.

Like this innovative way to settle an age old controversy – that of whether brain cells can form anew after birth it is a well known fact that brain cells once formed are not made again. unlike say for example the skin cells which are shed and then replaced. (Actually we go through a new skin every 1-3 months.)

But research in the early 70’s showed that we actually make new brain cells even after we have grown up. (the technical term is adult neurogenesis).

How is this done? In animals you give them stuff called BRDU which gets in the DNA of the cells. Now a cell only makes new DNA once ie when it is forming. Therefore only those cells take up DNA which are being born. If you look for which cells have taken up BRDU you know these are the cells which have been born after you gave the BRDU to them.

Does adult neurogenesis happen in humans at all? Can’t you give humans BRDU and see? Well no because BRDU is a mutagen. (causes mutations and therefore cancer). What would you do?

Well, here comes the innovation that works around this problem. In the period from 1955-63 there were a lot of nuclear bombs being detonated above ground for “tests”. This lead to the C14 levels in the atmosphere going up. In fact it follows a pattern with the levels coming down exponentially after 1963 when the test ban treaty was signed. This is shown in this graph.

(ignore the line and dot for now)


These ratios of C14 to the normal level would be reflected in the DNA of the cell as well because the C14 is all over the atmosphere which would get into plants and therefore into human food as well. When a cell is born this C14 would go into the nucleus as well. If you could measure C14 levels in the cell DNA you could tell when it is born.

You could do this for all the cells in body and determine the age of each groups of cells – like brain versus intestine. neat.

Next big question – Did it work? Did they show that new neurons are born in the brain after birth? did they? did they?

Well – short answer yes!


The vetical line in the year of birth of the indivudual(~1973). The red dots represent the date of birth of the cells of the different organs. The intestine cells (also have high turnover rates like the skin cells) are the youngest having C14 levels corresponding to being born in ~1995 while the cerebellar cells are the oldest – being born in ~1975.

The clincher here are the cortex cells being clearly born in 1982 or thereabouts, indicating clearly that new neuronal cells can be formed after birth.

Who would ever have thought that nuclear bomb testing would have such a scientifically useful fallout (pardon the pun). And yes truth is stranger than fiction.

For the ones who revel in the details here is the original paper.

(posted originally by samudrika)

Ramujan Prize for Indian mathematician

Just read on the BBC News site that an Indian mathematician, Dr. Sujatha Ramadorai of Tata Instititue of Fundamental Research has been awarded the Ramajuan Prize. She won it for her contributions to the ‘arithemetics of algebraic varieties and for her work on non-commutative Iwasawa theory‘. Congratulations doc!

Nice to see that it’s an Indian that won it, even better when it’s a woman. Women can do math Mr Summers! 😀

What’s not so nice is that TIFR’s website is so pathetic – no mention of Dr. Sujatha’s achievement, and absolutely nothing on her homepage.

This is one reason why post-graduates here know close to nothing about research being done in this country. The only research you hear of, and that can excite you is what’s happening outside. And if you happen to be one who is keen on getting a PhD, (and are sensible), you would head west.

Being in a quite optimistic mood today morning, I hope things will change, and soon.

BTW, if any mathematicians read this post, could you translate Dr. Sujatha’s work in pop-science language??

(originally posted by MadGenius)

Hello World!!

High time I did post here, before more people start doubting my very existence. Had planned initially to blog on something else, but that didn’t happen. That’s a long story, and I will not repeat it here.

As this is going to be an introductory post, I think I shall tell you about what I do. I work in a small bioinformatics based company in my hometown as a research associate. That’s my designation, although I don’t really do any research. What I do is ‘literature curation’ – a field which not many people in biology actually know off. What it involves is basically reading research papers, putting all that data together, and help improve biological databases. Once the data has been collated and meaningfully put together, it can be then used for finding drug targets, designing experiements, etc etc. This ‘collation’ of data can range from simple keyword/abstract indexing of papers to building signalling pathways in specific cell systems.

For more, have a look at these articles from PLoS Computational Biology. Last month’s issue had a very nice editorial on the role of ‘Biocurators’. I especially loved this-

Biocurators can be considered the museum catalogers of the Internet age: they turn inert and unidentifiable objects (now virtual) into a powerful exhibit from which we can all marvel and learn. That would be a decent enough contribution to the world of science, but the task of the biocurator is even more extensive. Computational biologists do not expect to merely walk through the door, cast a casual eye over the exhibit, and exit wiser (although we frequently do); we also want to add our own data to the exhibit, plus pick and choose pieces of it to take home and create new exhibits of our own. Oh, and we would like to do all these things with minimal effort, please. We can be a pretty exacting bunch of customers, and it takes skills over and above a knowledge of biology to juggle the different needs of data submitters, information seekers, and power players.

This wonderful article gives a comprehensive description of a curator’s job while dealing with a (slightly) static database, while this one describes how data can be put together to create a (more dynamic) interaction database.

(originally posted by MadGenius)

On Being a Grad Student

If you’ve been following this blog for a bit you’ve obviously noticed the little strip of the latest PhD comics along the top.

PhD Comics is written and drawn By Jorge Cham, a one time grad student at Stanford University and used to be published in their student newspaper but now appears in a number of newspapers across the US as well as on the web.

One of my favourite series of strips is the Star Wars sequence because it appeals to the geeky side of me too! (Like grad students are not geeky enough!)

Oh, did I mention there was a Matrix series too?