The conduct of science: Organic change

Most scientific research is about incremental improvements to existing theories. Every so often, though, an anomaly shakes things up, offering upstart ideas the chance to dislodge reigning ones. In December 2010 NASA, America’s space agency, announced a discovery which would, if confirmed, engender just such a shift. Their paper, published in Science, reported the isolation of a new species of bacterium. Where DNA of all known organisms is built on a backbone of phosphates, derived from phosphorus, GFAJ-1, as the microbe NASA’s boffins found in Mono Lake, California, is known, instead sported arsenates, chemical compounds based on arsenic. Since arsenic is toxic to other lifeforms, that would make the microbe different from anything else found on Earth.

Within a week of publication, however, scientists around the world began poking holes in the study. Its extraordinary and, they felt, unfounded claims called for extraordinary measures. So rather than pursue the usual, lengthy process of submitting papers to journals, which send them on to specialists in the field for formal evaluation, they tore the study apart in blogs and on Twitter.

In response, NASA scientists hid behind peer review, as the time-honoured practice is known, insisting they will only entertain such “formal” criticism. They can hide no more. Last week Science published two papers outlining failed attempts to replicate the results.

The first, by Tobias Erb, a microbiologist at ETH Zurich in Switzerland, and his colleageus, shows that even though GFAJ-1 can indeed grow in remarkably high concentrations of arsenic, it nonetheless needs small quantities of phosphates in order to survive. This contradicted the original paper’s claim that the phosphates found in GFAJ-1 were insufficient to sustain life. In the second paper a team led by Joshua Rabinowitz, from Princeton University, and Rosie Redfield, at the University of British Columbia, reported the bacterium’s DNA contains traces of arsenic but that its role is not as central as NASA’s boffins had claimed.

Dr Redfield, an early and vocal critic of the arsenic-life hypothesis, has blogged about her findings over the past year. The paper she and Dr Rabinowitz had submitted to Science has been available for months on arXiv, a free online repository. This is unusual; researchers wanting to reveal their full finding prior to publication in Science and other leading journals which charge hefty subscription fees for providing access to the world’s best research need special dispensation from the publisher to do so.

This policy is looking increasingly unsustainable (see article in this week’s print edition). Peer review takes months and requires journals to act as intermediaries. The internet means that research can be subjected to unofficial, but no less diligent, scrutiny in a matter of days. Physicists and astronomers, the primary users of arXiv, have long since embraced this new model. Nowadays, a paper’s publication in a prestigious physics journal serves merely as a stamp of approval, not a way to disseminate findings. The arsenic-life palaver demonstrates that other disciplines are beginning to follow suit.

Also published on


  1. Wolfe-simon et al.Science, 2011
  2. Reaves et al.Science, 2012
  3. Erb et al.Science, 2012
  4. Scientist in a strange landPopular Science 2011
  5. Redfield on NASA’s claimsRRResearch 2010
  6. Redfield’s paper on arXiv, 2012

 Image from here.

The internet, social media and relationships

Whenever I sign in to my Facebook account, I am greeted by hundreds of smiling faces wanting to tell me about their lives. I can at the choice of my whim get entertained by my friends doing stupid things or choose to wonder about the beautiful world through that friend’s pictures who just spent the last month in New Zealand. I can feel nostalgic by hearing that old song which was posted by another friend or even choose to cry reading about the sad story of a friend who met with an accident and who’s ‘wall’ is full of messages from well-wishers. I can choose to feel jealous about my mate who just found the hottest girl-friend or go to the profile of my class topper and get a dose of Schadenfreude from knowing that he is on a minimum wage job. I have the whole platter of emotions served to me everyday at whatever time I would like.

The cherry on top of this platter is that I also have the choice of declining to listen to any of these stories without it being considered rude. It’s great. Even King Louis XIV could not afford this kind of social luxury with all the power and money he had.

We live today with hundreds of friends on Facebook and similar number of followers on twitter. We have the ability to broadcast are thoughts in words, written or spoken, to millions of people for free. I can build friendships across the seas and over the mountains. I can have intellectual debates or learn something that blows my mind away. I can buy gifts for my parents sitting at my desk at work. The Internet has made plenty possible and yet I can’t stop but wonder when I heard the following from my dad.

“I was at your aunt’s place the other day and had a somewhat surprising experience. I was chatting with your cousin and asking her about her work. She explained it well in detail and we had a nice chat which was interrupted only because she had to leave. When she left your aunt came to me and told me, ‘You know she has never before explained to me what she does at work, despite having asked many times before.’ On further enquiry your aunt explained that she spends most of her time at home on the computer. She’s either on Facebook or watches some videos on YouTube. Rest of the time she doesn’t talk much. And I could not disagree because this was the first conversation that I had had with her in many years where she answered in more than a few words.”

I know my cousin somewhat well. We used to have lots of fun as kids but it has been many years since we spent any substantial time together. I know that she is a smart girl and although I can’t say much about her conversational skills. It makes me wonder that if the social media revolution had happened while I was still at home, would I have fallen in to the same ‘trap’ – showing a lack of interest in the people around me but paying more attention to those on Facebook. I tried to dismiss it as a singular case but my dad retorted that it is not a singular case. He’s heard the complain from many other parents in the recent months. More importantly though, the case my dad described was of an urban Indian family. In India, Facebook hasn’t quite reached the levels of penetration that it has in the US or UK.

The information diet

I have had a blog post in the drafts section for some time now, it is titled ‘rethinking our digital lives’. I will publish it some day soon but what actually got me thinking about writing that post was the fact that all of us spend a lot of our time on the internet. It may be for work or pleasure, doesn’t matter. The fact is that the ease of opening a new browser window or tab means that distractions are only a click away. That’s been a bit a of a problem for me and I suspect for many others. Something needs to be done about that and so I’ve decided to go on an information diet.

Here’s what I am going to do:

  1. Check email only three times a day.
  2. Check facebook and twitter once a day for not more than 30 minutes in total.
  3. Check my blog only when I decide to publish something.
  4. Any article which I deem worth reading, I will send to my Kindle. Thus, I can get to it when I have the time.
  5. 30 minutes of video everyday including YouTube.

Being able to restrict social media won’t be that hard but to deal with email I am going to need some help because I essentially use it as my to-do list. I’ve installed Boomerang for Gmail which will help me schedule replies, bring emails to my inbox when they need to be dealt with, etc. For reading articles I’ve been using SENDtoREADER which simply re-formats the article like Readability and sends it to my Kindle.

Just like food, there is some information that is good for you and some that is bad. Being able to focus on the good in this world of distractions is a hard thing and that’s why I think there is much value in choosing to do this. My experience with dieting is only a recent one but along with my polyphasic sleep experiment it has give me enough confidence in my ability to discipline myself that I think I can take on this task.

Finally, unlike the slow-carb diet experiment, this will not be a four-week experiment. I want to make this information diet a habit so that the extra time I get are put in meaningful work.