The Arsenic DNA Bacteria that might not be!

Wednesday, 8 December 2010 02:54 by salim

So, earlier last week, NASA comes out with an announcement saying that it will have a press conference on the 2nd of December to announce a major development that has implications to astrobiology.

A day after NASA announcement, Gizmodo published a highly speculative article that predicted that NASA is going to announce that they have found life in one of Saturn’s moons. Then there was just a flood gate of article, some of them with completely bizarre and unfounded speculations and rumors about the discovery.

On December 2, 2 PM, NASA announces the finding (at the same time the article was made available in Science Magazine titled A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. The authors claimed in the paper and asserted in the press conference that they have shown that these bacteria can not only tolerate Arsenic but incorporate it into their DNA structure replacing Phosphorous.

This followed another flood of reports and blog posts. There was great excitement about the news, especially because it, if correct, would mean that the life can support a much wider range of conditions than we thought. It also will suggest that the main ingredients if life as we know are not that fixed after all.

First thing to come out of it was that, it was certainly over hyped by NASA by clearly hinting it is something more than what it is. Yes, finding a life form that can substitute Arsenate instead of Phosphate is an incredible finding. But, we know life on earth is very resilient and innovative. It would certainly don’t mean that we are closer to finding exobiological entities.

Along with this, there came a series of posts by scientists questioning the veracity of the methods used by the NASA scientists (Felisa Wolfe-Simon et al). Among the many I read about this subject there are two that stand out in its clarity of presentation and scientific rigor (no, that is not to make any claims about its correctness).

The article by Alex Bradley looks at the problem from a chemist’s perspective and brings up a few very serious process and interpretation issues. He correctly points out that there were due diligence that the NASA scientists did not perform.

An even more detailed criticism by Rosie Redfield can be read here. She goes more into the methodology and points out many potential pitfalls in them.

All this reminded me of the famous Carl Sagan adage “Extraordinary claims require extraordinary evidence”.

Another point this brings to light is the methodology of science and the immediacy and openness with which it is happening. Answering requests for comment, one of the authors of the article said that the discussion should happen in peer reviewed journals, not in the blogosphere. That is a bit odd though, considering that they themselves made an effort to make this very public.

Irrespective of how this particular finding turns out, science will go on. I have noted this earlier, the usually hidden away dynamics of the process of scientific enquiry is now spilling over for every one to see. It is beautiful, exciting. Now, if only the media learn to stop seeing everything in black and white.

 

My Dinner

Sunday, 31 October 2010 01:34 by salim

We both like cooking and eating good food. We both agree that we can cook better food than most restaurants. And our cuisine is pretty eclectic. However, some days we fall back to the nice Kerala style dinners. Today was such a day. When everything was on the plate, I couldn’t help but take a picture. So, here it is

My Dinner

Clockwise from left:

Green cabbage stirfry, green eggplant stirfry, snow peas stirfry, sardines shallow fried in their own oil, chick peas stir fry, tender mango pickle. In the middle of course is Kerala brown rice with sambar and curd (Yogurt).

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For all those grammar nazis around!

Sunday, 24 October 2010 11:15 by salim

Grammar nazis and language pedants get owned by Stephen Fry!

Stephen Fry Kinetic Typography - Language from Matthew Rogers on Vimeo.

(Got from Bad Astronomy)

Why I don’t like Kindle

Thursday, 28 January 2010 23:20 by salim

Kindle, Sony Reader and other less known e-readers were making a lot of noise lately, which is growing to a fever pitch by the advent if iPad. (I do think iPad will make a horrible e-reader just like a notebook/netbook because of the glossy screen unlike the electronic ink technology of other readers).

I have abandoned paper versions of books and magazines for quite some time, but i have not moved on to an electronic reader. I have been thinking about it, but almost always, i am sitting in front of a computer, and the time that i spend away from computer are when i want to engage my mind in non-intellectual activities. So, while it was a very attractive device, I did not buy it, yet.

So, when Amazon decided to make a software version of Kindle, I was very happy. One of the drawback of being a full time electronic reader is the limitation of established content. It is very hard to get electronic versions of print books unless you are subscribing to one of these e-book thingies. So, I eagerly downloaded it and started using it.

The first book I downloaded and read was Darwin’s Origin of Species. It was free. It did not take me long to notice several major differences between reading Kindle and reading other on-line content. The second book, which I am still reading is Richard Dawkin’s God Delusion.

One of the reasons why I don’t like print media is its lack of interactivity. You cannot click on a link and hyperjump to a related article. You cannot just switch to another tab and Wikipedia or Google or Bing for more information about something you want to know more about. I have been catching myself looking for where to click when reading the magazines in the hospital waiting room.

The kindle electronic version does produce very nice looking pages. It is crisp. The size is changeable and it was quite easy to get it to an easily readable size for my monitor. However, once I started reading, I started seeing the same annoying limitations that I find with print media. The text is completely non-interactive. The only hyperlink is to the footnotes, and even full web addresses cannot be clicked on. So, I tried the next thing, try to copy the link address and paste it, but of course, you cannot copy text from it. There is your DRM at work. Soon I found that I cannot search the book either. All I can do is put book marks and jump to pages. It is like a nicely scanned print book!

Today morning, while we were waiting for her radiation at the hospital, Shobha suggested that I buy a Kindle or other reader so that I can read while waiting. But, I don’t think I will do that. I will just people watch the few minutes that I am sitting there. For me, the reading experience has moved away from the passive eye scanning. When I read, I want to control the content. I want to control the narration. I can do it in digital media, whether it is coming as a webpage or PDF or XPS. I can’t to it on the page of Better Homes (for some reasons, every hospital waiting room has Better Homes). I can’t do it on Kindle. I might be able to do it in iPad, but that is not a device for me. If i want to do all those things, I will get something with a higher resolution screen, a multi-core processor and a usable touch keyboard.

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War, peace and love

Friday, 22 January 2010 01:13 by salim

A wonderfully moving performance. I am speechless, and teary eyed.

Intel Commercials

Tuesday, 3 November 2009 00:01 by salim

Intel has been airing some very funny, brilliant commercials these days in their “Sponsors of Tomorrow” series.

What I like most in these commercials is the celebration of brainiacs, otherwise known as geeks. Below is the Ajay Bhatt commercial.

Our rockstars are not like yours

Even funnier one is the one in which one guy sitting surrounded by glass boards filled with equations. He gets up, changes a minus to a plus in one place and goes back to his seat. His colleague comes in with coffee, looks at the board and says “very funny”. The other guy chuckles uncontrollably! I cannot stop laughing every time i see that one. Unfortunately, i couldn’t find a version of it in the net.

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Earth A Biography - Science/Nature shows and religious determinism

Wednesday, 16 July 2008 00:50 by salim

The new three part series in National Geographic is one of the endless series of very high definition earth imageries that now fills the Science/Discovery/NG channels. This, like most other documentaries of the type gives a rather peripheral view of the earth and its evolution.

The series examines different aspects of earth's life through beautifully captured imageries, that rightfully stands at par with Planet Earth and Blue Planet.

I have not watched the whole of it yet. But from the three parts I have already watched, it feels a bit empty except for those gorgeous shots. Dr.Iain Stewart is not the most entertaining presenter if you ask me. But more than the presentation itself, it is the abundance of platitudes that kill the enjoyment.

Here is one example. The episode is Volcanoes and Iain is talking about the carbon cycle. The scene starts with really beautiful micro-shots and quite dazzling aerial and satellite pictures of the sea green with algae. Then he describes how algae absorbs carbon dioxide from the atmosphere and eventually die and sediment at the bottom of the ocean. Then comes the revelation! If the algae continues to absorb carbon dioxide, it will eventually thin out the green house effect and the earth will become too cold. That will be the end of life! He then continues to talk about the seduction as the tectonic plates move and the carbon in the sediment gets converted to carbon dioxide.

This is actually a constant theme in these science/nature shows. There is always this single overarching reason for life to survive. Reduce the temperature by a few degrees, a rogue meteor. This not just is limited to the destiny of life, but for the universe itself! Often you will hear if the value of cosmological constant was a bit off, or if the initial temperature of the universe immediately after the big bang was a little lower...

As I see it, these are the same fatalistic deterministic world views that is so ingrained with our age old views of the world, mainly controlled by theological dogma and mythological delusions.

Deterministic narratives of cosmology is fundamental to the propagation of religious dogmas. Any assumption of creation - as Einstein amply demonstrated - has to preclude any questions about a deterministic evolution. Remember, god does not play dice!!

We should, by now, know that there is not just one path that leads to the current state of the Universe. While past might be fixed, it does not, by any means say that this is the only possible current state. Nor does it mean that our past is the only way to reach here.

I am eagerly waiting to see a narration that is devoid of the fatalistic proclamations one of these days. May be I should watch Nova more regularly!!!