I Wish That I Could Turn Back The Clock

A superb paper on the importance of historical contingency in the evolutionary process just came out in the latest issue of PNAS.

This study was done to address an old quibble between Simon Conway Morris and Stephen Jay Gould about what would happen if we could return to the prehistoric past and replay the evolutionary process again.

Will natural selection result in organisms that look fairly similar to what we have on Earth today, or will a series of unpredictable happenstances result in new organisms that look utterly different?

The Lenski group at Michigan State University spent 20 painstaking years to perform this study - I must say that I'm impressed with both the simple elegance of the experimental design and the sheer dogged tenacity of the research team.

I don't have enough time now to write a comprehensive summary (see Pharyngula's excellent post), but just to give you a flavour of what they achieved:

12 separate populations of E. coli bacteria (which normally cannot use citrate as an energy source under oxic conditions) were grown in identical citrate-rich environments for over 30,000 generations.

They froze a sample of each population every 500 generations to act as their "fossil record" so that they can rerun the experiment from that stage, if required.

All 12 populations had been experiencing a declining rate of fitness improvement.

Then, at the 33,127-generation mark, one of the populations was observed to have evolved the ability to use citrate. None of the other 11 populations can do it, not even till today (>44,000 generations).

"Replay" experiments using stored samples earlier than the 20,000th generation were completely unable to yield any citrate-using populations.

In striking contrast, some of later samples easily evolved citrate use within a few thousand generations.

Thus, this evolutionary innovation is produced by mutational change. Natural selection only plays a secondary role in preserving the changes.

Would you like to know more?
- Original research article: Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli (Blount et al. PNAS)
- Historical contingency in the evolution of E. coli (Excellent summary at Pharyngula blog)

Benefits Of Failure, Importance Of Imagination

Novelist J.K. Rowling, author of the best-selling "Harry Potter" series, gave this entertaining and powerful commencement address at Harvard University a few days ago.





Not a fan of the fantasy genre myself (prefer spacey stuff), but Rowling's speech is a measured retrospective of personal setbacks and triumphs that is a refreshing departure from the usual "reach for the skies tiger!" kind of crap that passes as motivational talks nowadays.

My favourite part is:

So why do I talk about the benefits of failure? Simply because failure meant a stripping away of the inessential. I stopped pretending to myself that I was anything other than what I was, and began to direct all my energy into finishing the only work that mattered to me.

Had I really succeeded at anything else, I might never have found the determination to succeed in the one arena I believed I truly belonged. I was set free, because my greatest fear had already been realised, and I was still alive, and I still had a daughter whom I adored, and I had an old typewriter and a big idea. And so rock bottom became the solid foundation on which I rebuilt my life.

Nice.

Pipette tip to BackStage.

Would you like to know more?
- Complete transcript and video (Harvard Magazine)

On The Shoulders Of Giants

Pioneering Singaporean scientist Dr. Lee Kum Tatt has passed away on Sunday, the 1st of June, at the age of 81.

Dr. Lee was the founding chairman of the Singapore Science Council in 1967, helped to establish the Science Centre and Science Park, and invented the RISIS orchid in 1976.

In his blog, Dr. Lee drew from personal experience to offer words of encouragement and advice to the young people who are struggling to find their own path in the world today:

Our youngsters are looking for guidance on how to succeed in life. Encouraging them to go for money is easy. Teaching them how to earn money in the correct way is a different matter. To teach them good values in words is also not difficult. Some common words used include: love your parents; have integrity, be caring for others, avoid the four vices etc; But to teach others how to live these values is not so easy. This is especially so when our society places strong emphasis on money making above everything else. To do anything different from the newly introduced acceptable norms will cost our young opportunities, effort, money, fun and with no materialistic or other tangible returns.

Fresh Brainz salutes this industrious and insightful chemist who was a key player in the inception of our scientific enterprise in Singapore.


Would you like to know more?
- Dr. Lee Kum Tatt's Blog

Counterintuitive Science: How We Know That We Don't Know

You know, sometimes when I am too demoralized to get out of bed in the morning, I like to play this little game.

I'll blink each of my eyes in turn to locate where the blind spots are in my visual field.

You can try this too - all you need is a plain, light-coloured background (such as a ceiling) to stare at.

The blind spots appear as a round, slightly dim patch near the centre of vision: left-of-centre (approx. 10 degrees of arc) in the left eye and right-of-centre in the right eye.

Once I find the blind spot in one eye, I will close the other eye and then raise a hand to try use my blind spot to "see" my fingertip.

As I move my fingertip into the visual area covered by the blind spot, it disappears.

A tip-less finger!

That's not so surprising - since there are no light receptors at the blind spot, no visual information is sent from the eye to the brain.

The weird thing is that the blind spot doesn't appear black.

It always takes the colour of the background - if the ceiling is yellow, the blind spot appears yellow too.

The brain is responsible for this effect.

In fact, even if the background is some complex pattern, the brain can still "fill in" the complex pattern over the blind spot!

Not convinced? Check out this flash applet and try it for yourself.

The blind spot has always fascinated me: how we can somehow "see" that we can't see.

Even more amazingly, we can also "know" that we don't know!

Like when you try to recall the name of someone familiar, but just can't quite remember it? You are pretty sure that you have that memory somewhere, but yet you can't access it.

Psychologists studying this phenomenon, known as the "tip of the tongue" state, have uncovered many surprising insights into the mechanism of human memory.

It turns out that information storage and recall are actually two distinct processes. In addition, the storage of what we consider as one set of information is really fragmented into many different locations in the brain.

Memory recall is highly dependent on the connectivity between these brain regions.

Here's an excellent article in the Boston Globe that describes the details of this strange effect:

The messy reality of the mind contradicts the conventional metaphor of memory, which assumes that the brain is like a vast and well-organized file cabinet. According to this theory, we're able to locate the necessary memory because it has been sorted according to some logical system. But this metaphor is misleading. The brain isn't an immaculate file cabinet - it's more like an untidy desk covered with piles of paper.















People with certain brain injuries can suffer from a permanent form of the "tip of the tongue" state, such that they can remember almost everything about a person - except for her name.

Hey, that sounds extremely familiar!

It's like an endeavour where scores of idealistic, hapless young turks spend years of fruitless labour on the verge of a huge breakthrough discovery, but never quite getting there.

I can't remember the name of that field.


Pipette tip to Mind Hacks.

We Have Always Done It That Way

If I have to pick one word that can sum up the human condition it would be:

Contingent