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“It suddenly struck me that that tiny pea, pretty and blue, was the Earth. I put up my thumb and shut one eye, and my thumb blotted out the planet Earth. I didn't feel like a giant. I felt very, very small.” – Neil Armstrong (1930-2012)

Fresh Reads from the Science 'o sphere!

Tuesday, September 23, 2008


I'm busy with some important experiments.

See you in December!

Wednesday, September 17, 2008

Bruce Alberts At The Biopolis

Bruce Alberts, who is the Professor of Biochemistry and Biophysics at University of California San Francisco, gave a talk at the Biopolis yesterday.

Prof. Alberts served two terms as the President of the National Academy of Sciences from 1993-2005, and is one of the original authors of the "Molecular Biology of the Cell" textbook (affectionately called the "Alberts" textbook by undergrads). He has been the editor-in-chief of Science magazine since 1st March 2008.

He was also the PhD supervisor of one of the top science bloggers, Larry Moran.

His talk is entitled "Biology past and biology future: where have we been and where are we going?"

He began by commenting that the situation in the USA is a bit crazy now, and hoped that things are more rational here in Singapore.

Then he presented an outline of his talk, which is divided into three parts: a review of his personal history, a discussion about the central role of protein machines, and his experiences on textbook writing and how they relate to new challenges for the biological scientist.

Here are some of the highlights in his talk!

1. Prof. Alberts mentioned that he was a high school student when the famous Watson and Crick DNA model appeared in 1953.

The next breakthrough, which he felt was also very important, was the discovery of DNA polymerase by Arthur Kornberg in 1957, who was later awarded the Nobel prize for his work.

Later, for his PhD thesis, Prof. Alberts decided to investigate if DNA polymerase alone can replicate DNA.

The result - it didn't work!

Consequently, he was the only student in his batch at Harvard to fail his PhD exam and had to retake it again.

This unpleasant experience was a wake-up call for him and this failure taught him two important lessons - that theoretical biology was more difficult than expected, and that having a good research strategy is the key to success in science. He cautioned against approaches with a "yes or no" answer; instead he recommended planning experiments where any answer will help advance scientific understanding by at least a small amount.

He also emphasized the importance of learning from failure, and that young people should be allowed to fail. He stressed this point a few times during the talk.

2. Next, he discussed some molecular details of the DNA replication process. Prof. Alberts felt that DNA polymerase is an amazing enzyme and presented videos illustrating the replication process.

Here is one of the videos:

DNA replication involves at least 7 proteins (7 in phages, 13 in bacteria and 27 in human beings), which is the reason why Prof. Alberts' initial experiments failed.

After his PhD, he worked out a new strategy and invented a technique for isolating the proteins required for DNA replication. Using his new method, he discovered the first single-stranded DNA binding protein in 1970.

He then went over some details of other protein machines that are powered by ATP hydrolysis.

He emphasized the importance of biochemical approaches such as activity assays, which is not commonly done in genomics labs.

3. After that, he talked about some insights he learnt while writing the textbook. He put up a photo of the manuscript, showing numerous corrections by the different authors to illustrate how messy the process was.

He revealed that one of the co-authors, James Watson, had grossly underestimated the time required to write the book, thinking that it can be done over the summer. Eventually it took more than a year, working 16-hour days, in order to finish the textbook.

While revising the textbook in recent years, Prof. Alberts observed some surprises in the research literature: that there are many functional DNA sequences that do not encode for proteins, that positive and negative feedback loops underlie nearly all of cell chemistry, and that extensive scaffold networks produce sub-compartments inside a cell without requiring a membrane.

He pointed out that there are about 35,000 highly conserved non-coding DNA sequences in the human genome with an average length of around 200 base pairs each. The biological activities of most of them are not yet known. He felt that more biochemists are needed to help study these.

Talking about the feedback loops, he noted that there is no way to understand these without mathematics, and thus physicists and computer scientists are needed to help study these. He emphasized the importance of starting with simple model systems, such as yeast.

As for intracellular compartmentalization without membranes, he highlighted the examples of the nucleolus and Cajal body. Current research suggest that cellular components such as these are transported to specific locations within the cell via "positional codes", and Prof. Alberts noted that this is markedly different from the previous concept of proteins randomly interacting with each other back in the 1960s.

Then, he discussed three important roles of biology: to inspire, to design intelligent strategies for improving human health, and to investigate the origin of life (what we can learn from Mars!).

To underscore the role of science for inspiration, he highlighted this quote from Richard Feynman:

The world looks so different after learning science. For example, trees are made of air, primarily. When they are burned, they go back to air, and in the flaming heat is released the flaming heat of the sun which was bound in to convert the air into tree, and in the ash is the small remnant of the part which did not come from air that came from the solid earth, instead.

These are beautiful things, and the content of science is wonderfully full of them. They are very inspiring, and they can be used to inspire others.

To sum up, Prof. Alberts observed that biology in the past 50 years has made successful inroads into understanding the molecular basis of life, but we still need to decipher the pathways involved.

In the future, the focus will shift towards "emergent properties" - properties that stem from complicated networks of chemical interactions, where understanding each individual part cannot illuminate the overall process. New methods and approaches will be needed before we can claim to understand even the simplest cells.

He stressed that there are many challenges for young scientists and encouraged them to "be ambitious!"

4. Then, it was time for the Q&A session.

The first question from the audience was about the difficulty of learning anything robust in biology, due to the complexity of the systems involved.

Prof. Alberts recommended that it is crucial to plan a model system, especially simple organisms such as phages and E. coli, and to focus on one subsystem of a problem. More focus would be helpful.

The second question was a discussion about the risk adverse climate in scientific research. Prof. Alberts noted that in the USA, scientists tend to submit grant proposals that will work - that is, they avoid risky projects. Science has become too conservative, and he thought that people should be given a chance to fail. "Good failures" should be rewarded.

He felt that the current method of evaluating a scientist by the number of published papers is having a negative effect, but acknowledged that top journals such as Nature and Science are "part of the problem". Science magazine alone receives over 12,000 submissions per year, so it is very difficult to select papers for publication.

Next, Prof. Alberts expressed his concerns over the continued fragmentation of biology. He wondered if there could be a "Department of Nucleolus" in the future and if biology textbooks 50 years from now would still be readable.

One member of the audience then asked: "How do you think that science education can be improved?"

Prof. Alberts said that he wasn't familiar with the Singapore system, but he felt that the "No child left behind" policy in the USA is having damaging effects. He observed that in politics, one has to be "right" - education policies are very dogmatic in the US and will benefit from more research on the education system itself.

To illustrate this, he said that his grandson is currently studying a science course at grade school and had to memorize parts of a flower. When Prof. Alberts asked him if he had actually seen the flower, he said no. Not surprisingly, his grandson hated that course - he preferred a course in ceramics instead, where he can create something by himself.

He felt that they were doing a horrible disservice to young people by making science a chore, and emphasized that "memorizing words is not science".

The last question was about the role of physicists, computer scientists and engineers in biology. Prof. Alberts reminded the biologists in the audience to keep their colleagues informed, and that it is not trivial to explain what is important and what isn't to the non-biologists who are part of the research team.

5. Before he left the room, Fresh Brainz managed to ask Prof. Alberts two questions relevant to the science' o sphere:

a) Do you see an important role for the Internet as a tool for science communication and education?

He felt that the Internet has been revolutionary for many aspects of society, but at present it is not very effectively used for science education. He revealed that the upcoming 2nd January 2009 issue of Science will contain a special feature on this topic.

b) Would you encourage more professors to write blogs?

He said that "some of them" should and agreed that Prof. Larry Moran writes really well.

Would you like to know more?

- BMRC Distinguished Visitor Programme

Monday, September 15, 2008

LHC Kumite

Physicists have really big toys.

Biologists, on the other hand, are usually satisfied with micropipettes, microscopes and the occasional automated sequencer.


(Pipette tip to Angry Doc)

Would you like to know more?

About the LHC:
LHC website (CERN)
Scientists turn on biggest ‘Big Bang Machine’ (msnbc)

About the LHD:
LHD website (NIFS)

Other LHC comics:
Collisions (Five-part comic by Jorge Cham)

Saturday, September 13, 2008

Kids Science Fest!

The Kids Science Fest! event is part of the science.08 festival and is held at the Annexe Hall 2 of the Singapore Science Centre.

Admission to this carnival is free, so if you have kids who are interested, you can still head there for a fun time tomorrow.

What do they have in store for you? Fresh Brainz visited the Science Fest today and uncovered a flurry of activity!

Here, a cheerful demonstrator shows some children how to prepare mini-rockets using fizzy Redoxon tablets, water and empty film containers.

I tried to catch a photo of a rocket in flight, but they pop up really fast and I could only capture a faint spray of water and the foam they leave behind.

Rocket fuel - now in delicious blackcurrant flavour!

There are a few workshops for kids to do some hands-on experiments. This young man is playing with a bowl of cornstarch mixture, which is a type of non-Newtonian fluid.

Really odd stuff - if you treat it gently, it will flow like a liquid, but if you strike it hard, it will react like a solid.

Just like human beings!

Cornstarch can behave in bizarre ways when put under constant vibration. Check out this video that shows you how it can transform into a teeming mass of disgusting "alien fingers".

If you are not into wet stuff, here's a dry workshop for learning about electrical circuits and electronic components.

The theme of the carnival is about speed and reaction time, so here's a game to see how fast you can shoot hoops.

This slope lets children try out different combinations of weight and wheel size for the toy car to roll down at maximum speed.

The "Save the Marbles" game also uses an inclined plane - colourful marbles roll through a regular array of plastic pins randomly, and the player tries to catch as many falling marbles as possible using a sliding bucket.

Any player who manages to catch more than 30 marbles gets to sign her/his name on a "Board of Fame".


Here they come!

*tik tik tik...*

In addition to workshops, there are also stage games - for the kids to participate in quizzes and maybe win a prize or two.

Looking a bit out of place is this small, dark alcove featuring some medical imaging panels.

There seems to be many MRI scans of brainz in here.

Which reminds me: it's time to catch the science show!

The "Think Quick!" science show is presented by Alan Gill and Bron Veale from Scitech in Perth, Australia.

Here's a huge brain prop sitting quietly in the foreground while Bron and Alan get ready for the show.

As a neurogeek, I am duty-bound to inform you that this brain is not anatomically accurate; the gyri are modelled haphazardly, it doesn't appear to have a temporal lobe and the cerebellum is too small.

I know you don't care.


Alan starts off the show with an introduction about how we are all different, but our brainz work in a similar way.

Notice those balloons in the background? To test our reaction time, the audience has to clap twice whenever a balloon gets popped.

(To find out where some additional balloons are hidden, check out the previous photo).

For a science show it certainly has many elements of drama. The two presenters adopt an "odd couple" approach and engage in bickering and one-upmanship to entertain the audience.

Here are some of the highlights:

Alan offers to help Bron relax.

"First, let's measure your blood pressure!"

"And here's a balloon for you! Close your eyes and imagine yourself on an island... in the middle of an ocean... surrounded by palm trees..."

*sneak sneak...*




As you can see, this is not a relaxing science show.

In fact I think it is the most energetic science show I've seen so far. Here's Bron running around off-stage to demonstrate that an athlete must have a quick mind as well as a nimble body.

Next up - memory test!

How many faces can you remember?

"Who is this?"

Christopher Lee!

The presenters have adapted their show for the Singapore audience by putting up ten familiar local faces.

"Have you seen this man?"

Bet you didn't see that coming.

It turns out that people can only hold a small amount of information in their short-term memory - around seven items at a time.

Most people cannot remember all ten faces. I can only recall eight names now.

So how can you memorize huge amounts of information? Take for example the exact value of Pi, which is made of decimals that don't repeat and go on forever.

How to tackle such a large task?

Break it down into many small chunks, why of course!

I should mention that when I was in secondary school, the school invited some whiz-kid from the USA to "inspire" the students.

To demonstrate his intellectual superiority over the rest of us, he recited Pi to thirty-plus decimal places and we were expected to applaud and be in awe.

My fellow classmate snickered: "He could be making it all up. Who would know?"

Besides, what is the purpose of memorizing Pi? A party trick?

If you really want to impress - make a bizarre discovery, cure a disease or invent a longer lasting light bulb.

Now that we know the usefulness of chunking data, let's try the memory test again...

"Who is this?"

Brad Pitt!

Angelina Jolie!

Technically, Brangelina should be regarded as one functional unit.

Darth Vader!

Surprisingly there are many kids who are familiar with Star Wars characters - looks like the prequels have exacted a severe toll on the younger generation.

Larkin: "I look forward to working with you, Lord Vader".

Vader: "You're beautiful..."

Admiral: "Vader?"

Vader: "What?!?? Erm... I mean erm... destroying the rebel base will be a beautiful victory!"

Admiral: "Quite, Lord Vader. Please continue."

Vader: "What?!??"

Star Wars has been spoofed to death a thousand times over.

By chunking the faces into groups it becomes easier to remember them.

This kid in orange could recall eight names: "... plus that guy who looks like you."

Alan: "You mean Brad Pitt?"

Bron: "You don't look like Brad Pitt!"

More odd couple moments...

The presenters asked for two volunteers to help with their demonstrations.

Here, the children clap their hands once and Bron has to point towards the direction of the sound with her eyes closed.

So far so good.

Then Alan makes Bron wear this ridiculous looking rig that switches over the left and right direction of hearing.

Quite a struggle now...

It's time for Alan to perform his demonstration!

The young volunteer throws a tennis ball at Alan and he catches it with no difficulty.

In retaliation, Bron gets Alan to wear inverting glasses while trying to catch tennis balls.

Oops... it's impossible!

During one of the throws, the volunteer actually managed to hit Alan on the face with the ball.



Finally, one more demonstration - the ability to read jumbled words, an observation that is often attributed to research conducted at Cambridge University.

A simple statement of truth?...

...of course they waste no time in resuming their fight...

And thus ends the show. I was ready to do some calping but I noticed that people were clapping, so I clapped instead.

Whew... luckily I was thinking fast!

After the show, Alan and Bron let some curious kids and parents try out their bizarre switcheroo gadgets.

Aside from the Kids Science Fest, I should also mention that there is a "Science of F1" exhibition in the Science Centre main building now. You'll need to pay the admission fee to enter the main building but if you haven't been inside for a while it's worth a visit (since the Dinosaurs are still around).

Here's an actual F1 racing car, on display for a limited time only. I like the speckled appearance of the carbon fibre wheel struts.

From behind you can see that the part of the car behind the driver tapers into a thin knife-edge.

Aerodynamics is critical when you are roaring along at over 300 km/h.

In keeping with the racing theme, a couple of FSAE racing cars from NUS are featured here.

Also on display is this fiery red Ferrari. Not sure why this is here, since it is a luxury sports car and not really a race car. Maybe it shares some technology with Ferrari F1 cars.

At around US$1,000,000 each it's not surprising that there are only two of them in Singapore.

I can never afford to buy one of these, nor do I want to.

Hmm... that suddenly reminds me of something!

A "vehicle" that I have which is also very rare and valuable.

The TIE/sa bomber.

Well, we were talking about Star Wars just now.

It's a vintage 1980 Kenner die-cast metal toy - apparently only 10,000 of these were ever made.

A mint-condition TIE bomber in its original packaging can fetch over US$1,000 in auctions. Well, I didn't buy this toy at age five just to NOT open the pack, so it won't be worth that much.

Still, it's a beauty.

Very few toys nowadays are made so detailed that they resemble movie props. Maybe that's a reason why these are so coveted.

As a parting shot, here's a close-up of the engines behind the bomber: not a 651-horse Berlinetta V12, but a pair of 125-KTU Sienar P-s4.


Would you like to know more?

About a previous science.08 event:
Science in the Gardens
X-periment! 2008