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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!

Thursday, September 28, 2006

101st Post!

Wow, would you believe it, in just two months Fresh Brainz has already hit 101 posts! Yes, it has been a pleasure writing for you, my friends!

*bows*

And in this celebratory mood today, I will blog about something light.

Like toys!

I just bought this toy recently.














It was sitting together with a bunch other education toys such as plastic dinosaur kits at a Popular Bookstore.

Of course I like dinosaurs too, but I bought this because I don't have a plastic model of a Cambrian animal yet. There is small selection of these.

I chose the Pikaia. I'll tell you why later, it's a nice story.

This is actually a small, pocket-sized toy that is really cheap, about four dollars. I like the way they make the packaging look like a book (not terribly original though).





















Inside is a tiny booklet (written very simply for kids), the unassembled plastic model and an instruction sheet.

Just three pieces. It isn't brain surgery.















Viola! All assembled. It took like two seconds.

So now that I am the proud new owner of a Pikaia toy, you might be wondering - what's so special about it?

Actually there is nothing really special about Pikaia. It's just a small, extinct animal that lived in the ocean over 500 million years ago.

It wasn't the biggest, it wasn't the fastest, it wasn't the strongest and it certainly wasn't the most exotic-looking animal of its time.


















Compare it to the ferocious Anomalocaries. Ten times larger, with fearsome grapper arms and a huge disc-shaped mouth - a killing machine!

It's certainly true that Pikaia was a middling, boring nobody. But an important nobody nonetheless, because Pikaia (or its cousin species) is the ancestor of all living chordates today.

That includes vertebrates like you and me.

In contrast, many exotic Cambrian animals like the Anomalocaries have no modern descendants.

You think, "Hey! Didn't Darwin say that evolution was about 'survival of the fittest'? What the fuck is so fit about a tiny grey fish-thingy?"

Actually Darwin never said that - he knew that the hottest hunk cannot contribute to the future biologically if he makes no babies. Herbert Spencer was the one who coined the term "survival of the fittest".

Perhaps Pikaia was only super good at baby-making. We may never know.

Still, what I want to say is: don't be discouraged if you feel yourself below par in terms of your looks, your abilities or your wealth. What is more important is how well you adapt to your environment.

We human beings are lucky that we are mobile enough to move to another environment when the going gets tough. In a supportive environment, every ordinary person has a good chance to live a happy life.

To learn more about Cambrian animals, here is a good interactive website from UC Berkeley.

Cheers!

Wednesday, September 27, 2006

Superb Computer Animation Of A Cell

Creative people at Harvard have produced this animation of what happens inside a white-blood cell when it moves along blood vessel walls.


It's quite accurate and looks very dramatic. See how many cellular processes you can identify!

The Stuff Of Nightmares

We at Fresh Brainz have never really understood the human attraction to the macabre. But yet I can't say that I disapprove of it, I wonder why...















These dolls are expertly hand-made to draw your attention and creep you out at the same time. They are obviously not recommended for children, unless you're from the Addams Family.

Just put one in your bedroom to enjoy a long, sleepless night! Cheers!

Finite Improbability Drive

No, this is not about the Hitchhiker's Guide to The Galaxy, but it's something true to its spirit.



Fucking amazing, if you ask me.

Tuesday, September 26, 2006

Big Debates

Just came across this great new program from the Canadian Broadcasting Corporation (CBC) called The Big Picture. Click on the link to watch the videos.

It's hosted by journalist and documentary film-maker Avi Lewis.

The format of the show is: prominent guests are invited to watch a documentary relevant to current affairs, and then debate on its central topic.

The discussion can get really heated at times, but the host keeps it civil and many interesting opinions are expressed.

This is a high-octane debate show. I find it hard to watch at times, but overall I think it's a superb program that examines issues that matter deeply to people.

Network Woes

The network in our institute has become so slow recently, it's utterly ridiculous. When searching online databases the screen would sometimes turn blank for several minutes. Pages can take minutes to load or fail to complete loading.

Frustrating.

Sunday, September 24, 2006

Yoda Spears







I... erm... I... hmm.

Drawn And Quartered

In this second part of my creature-feature I will introduce to you: the planarian.

Remember in the movie Men In Black, there was an alien shopkeeper who gets his head shot off and then grows it right back?

In the real world there is an animal that can actually do this. The planarian flatworm.













These creatures have a permanently "cross-eyed" look that is just plain funny. But more than just amusing, these guys are also amazing.

If you take a planarian and cut it into two, the head part grows a new tail and the tail part grows a new head.

If you slice it lengthwise, it can still grow into two animals. In fact, you can cut it into eight pieces and they will all grow into new worms!

You think, "Heh, big deal, these worms are simply made up of some kind of mushy meat that is all the same anyway, so who cares how you cut it up?"

Not quite.

Although simpler than vertebrates, planarians do have specialized tissues and organs. In order to grow a new head, the wound region has to somehow de-differentiate into a growing mass of cells and then re-differentiate into new target tissues.

Now that is pretty hard to do.

Even more bizarre, if you try to starve the planarian worm it will shrink in size. Not just lose some fats like people would, but all of its organs will actually shrink in unison and carry on functioning as if nothing happened. When you feed it again, it will grow back into its normal size. Of course if you push it too far it will eventually curl up and die.

Planarian worms are not the only animals that exhibit regeneration. Simple marine animals like echinoderms and starfish can also do it, to a lesser extent. So can earthworms, cuttlefish, salamanders and axolotls.

In fact human beings have limited regeneration ability - in repairing skin and muscle damage, and more significantly in repairing liver damage. A human liver that has been cut into one-third its normal size can still grow back to full size. Too bad this doesn't work for other organs, and limbs.

Still, planarians trump us all. Their incredible ability to regenerate is the reason why they are closely studied by scientists who hope to learn their secrets and apply this knowledge to people with limb injuries. We already know that there are some key genes involved in this ability. One of the prominent scholars in this field, Dr. Alejandro Sanchez Alvarado of the University of Utah, came to Singapore two months ago to give us a talk on his research.

I think the existence of such animals remind us that human beings are not the "epitome" of evolution. The more we learn about other animals, the more we realize just how normal-normal our own physiology is.

Schm-arty Farty

Just a few days back a new sculpture was unveiled amidst much fanfare at Biopolis, where my lab is.

Sculpted by Mara Haseltine, it's called "Sars Inhibited" and is supposed to depict a part of the SARS virus protease. Big arty sculptures tend to be expensive, and this one is no exception.

It costs as much as a luxury car. Or in science-speak, enough money to fund three graduate students for four years.

Here, I'll show you what it looks like.
















Basically it's a three-piece installation, made of twisted bronze, set in an existing water feature and complemented by special lighting underneath. At night it has a beautiful shimmering quality, but in the day without mood lighting it looks rather basic.




















I think that its smooth texture and graceful curves demonstrates the excellent worksmanship of the sculptor. Whoa, I can see my own reflection!

Having said that, I do have some thoughts.

Just one tinsy issue.

During the unveiling ceremony, Mara was interviewed by the local papers and she said that:

I'm obsessed with natural beauty and how it's created. So Sars was very difficult for me because I found it hideously ugly and twisted.

I won't (and can't) argue aesthetics with an artist. But when an artist talks about science, I have things to say.

This is what the SARS virus looks like.

Personally, I don't think it's ugly in appearance, in fact it reminds me of one of those Koosh balls that were so insanely popular in the '80s.

But ugly or not, there is nothing twisted about it. It just looks like a spikey ball.

Of course, Mara may be referring to the SARS main protease alone, instead of the whole virus. Proteases are enzymes that act on other proteins. After the SARS virus invades a host cell, it uses its main protease in the process of making new viruses, so inhibiting its function can stop the viruses from multiplying.

In fact Mara's sculpture is supposed to depict part of the protease that an inhibitor molecule, designed by scientists, can bind to and disrupt its activity. Here is a picture of the whole protease.

You can see that it does have a twisted appearance, but that's simply because the protease is displayed using the "backbone" (or ribbon) representation to help researchers clearly see its three-dimensional features, such as alpha helices and beta sheets.

Using this display format, all proteins appear twisted.

Even haemoglobin, the protein that carries life-giving oxygen in our red blood cells.












SUPER twisted.

However, there is another commonly used display format called the "space-filling" representation. This is actually a closer representation of the actual shape of the protein. If you use the space-filling representation, the SARS main protease starts to look like a delicate coral.











Not in any way twisted.

I think this picture is especially nice because on the right side of the protease you can see how the backbone representation sits inside the space-filling representation.

So to sum up - saying that SARS is ugly because it looks twisted in a backbone representation, is like saying that Antarctica is ugly because it looks "long" in a Mercator projection map.


OK, this discussion may sound really picky and irrelevant to artists. But I realize that feelings are important when they create their works of art, so it's helpful to have a fair understanding of their object of interest in order to generate the "right" kind of feelings.

To me, the SARS protease is not inherently uglier or prettier than any other protease.

It is more chilling to consider how something so tiny and so boring-looking can be an integral part of a deadly killing machine.

And uplifting to realize how an even tinier and more boring-looking inhibitor molecule can stop it in its tracks.

Saturday, September 23, 2006

The 30-Cent Chocolate Rule

You probably don't know this, but I am the sole caretaker of our research group's chocolate jar program. Chocolates are the lifeblood of graduate students (and techs and postdocs and scientists) so it's my job not to let them see the cold, empty bottom of that jar.

Since I have been replenishing the chocolates weekly for several months now, I have become a bit of a chocolate-shopping expert.















Recently I've suddenly noticed that the price of chocolates per piece is rather similar. I call it the 30-cent rule since they seem to average around 30 cents per piece. Here's my (limited) data so far:

Price per piece

Low
Van Houten Neopolitans - 8 cents

Medium
Delfi Top - 24 cents
Cadbury TimeOuts - 25 cents
Mini Toblerones - 26 cents
Kinder Chocolate - 26 cents

High
Ferrero Rocher - 31 cents
Cadbury Dairy Milk - 35 cents
Mini Snickers - 41 cents
Mini Mars - 41 cents

I find it surprising that Ferrero Rochers, despite their gold foil wrapping and generally high-class packaging, are actually so aggressively priced.

Anyway I will be updating this post when I buy other brands of chocolates to see if any of them flout the 30-cent rule.

This just reinforces my deepest belief that happiness is not free, but it's amazing how inexpensive it is :D

EDIT: More chocolate prices have been updated. See above!

Thursday, September 21, 2006

Voley Voley Voley!

This is the first article of a two-part Fresh Brainz creature-feature where I will introduce some really interesting animals to you. But before I delve into the discussion, let me clear up one misunderstanding that people often have about molecular biologists.

1. Sometimes molecular biologists get asked about animals they study, and let's say one of them says "zebrafish". Her non-scientist friends might then say: "Oh, you like to study fish? What's so special about fish?" They might even refer to her as a "fish expert" and start bombarding her with trivia questions about fish.

Ok I won't deny that there are people who study fish just for sake of studying fish, like marine biologists or zoologists. But most molecular biologists are not interested in studying all aspects of one species of animal, like how fast the zebrafish swims, or what its predators is, or where its natural habitat is.

They are using that animal species as a model. There is something unique about this particular species that makes it suitable for studying something important to researchers. More often than not they want to investigate the features of the animal that are similar to features of human beings.

Of course your choice of model organism depends on what you what to know.

To learn about basic cellular processes, such as how proteins are made using the DNA code in a cell, bacteria are very useful.

Studying the control of gene expression is better done using yeast cells.

Understanding cell cycle progression (relevant to human cancers) can be done in frog eggs which are large and full of protein.

To find out more about birth defects involving the neural tube, researchers often use zebrafish. Of course, to learn about limb development defects you will need a model animal with limbs, like mice.

Each model organism has its advantages and disadvantages, for both scientific and practical reasons.

For example, the worm Caenorhabditis elegans is useful for genetic studies because it shares many genes with people. It is tiny, cheap to maintain, reproduces quickly, can be grown in a simple petri dish and you can study lots of them at the same time.

However, it is evolutionarily distant from people, and results obtained from worms may not be relevant to human beings.

Mice on the other hand, have 99% genes in common with human beings (95% sequence identity at the DNA level), so knowledge gained from mouse studies are far more relevant to people. In fact mice are very often used in medical research. However there are also drawbacks to using them.

Mice are larger, are more expensive, need more effort to care for them, have a much longer generation time and must be housed in a special facility.

Thus, one must choose a model organism based on its unique biology and other practical considerations.

2. Now let's talk about the unique star of this story: the Vole!

I think science is cool because we can discover that some boring, normal-normal looking things are really very strange. The vole is one of them.

Voles are small rodents that resemble mice. Like mice, they seem to be evolving at a faster rate than other vertebrates, but voles have taken this to an extreme. For one vole genus Microtus, 60 species have evolved in just 0.5 - 2 million years.

To put this in perspective, that is about 60 times the average speciation rate of other vertebrates!

In addition, they have a whole bunch of weird characteristics such as:

a) Within the genus Microtus, the number of chromosomes vary wildly from 17-64. Species within a genus usually have the same chromosome number.

b) In one species, there is a super-big X chromosome that contains about 20 percent of the entire genome. Much bigger compared to other vertebrates.

c) In another species, females possess large portions of the Y chromosome, which is usually only present in males.

d) In yet another species, males and females have different chromosome numbers, which is uncommon in animals.

And here's a final bizarre twist - despite these crazy genetic variations, all voles look alike! Yet there is no evidence of accidental matings between different species of voles. We can't tell them apart, but they know exactly what makes them distinct.

Far out, man.

You can read more about these amazing critters from this website. DeWoody Lab at Purdue University is studying voles in order to improve gene therapy techniques, ultimately for human medical applications.

Of course for a molecular evolutionary biologist like me, these animals are already a marvel by themselves. It would be fascinating to examine in detail how these animals are such speciation-machines (I suspect a unique modular organization of developmental hub genes), but luckily for you, this is not that sort of blog!

Whew... that was heavy stuff.

The next post will be fluff. I promise!

New Hominid Fossil - Selam

Researchers in Ethiopia have announced the discovery of a 3.3 million year old fossil of a female toddler belonging to the species Australopithecus afarensis. They have named her Selam. This is the oldest and most complete specimen of a hominid juvenile ever found.

To put this in perspective, fossils that old are rarely so complete. What is usually found are a few teeth or pieces of the skull. This find is even more remarkable when you consider that young bones are more fragile and thus less likely to be preserved over millions of years.

Click on the photo for more information from the journal Nature.

Insights About Thai Coup d'Etat

By now most of you are already aware of the coup d'Etat in Thailand. Politics is not my expertise, so I'll point you to fellow blogger Rana at Memory and Desire for unique and in-depth insights in the current affairs.

Wispy Ring Around Saturn

The Cassini spacecraft has discovered a new faint, wispy ring around Saturn.

I have no idea what the scientific implications are.

I just like the photos.


Click the photo above for more...

Wednesday, September 20, 2006

No Place To Stand

Tuesday, September 19, 2006

Monday, September 18, 2006

Mobile Computing

Saw this on my way to a class this morning.




Well, I... er... at least it caught my attention.

Sunday, September 17, 2006

Calculate Your Nerdiness!

Wow, nowadays you can even quantify nerdiness. The marvels of modern technology.



I am nerdier than 56% of all people. Are you nerdier? Click here to find out!

I guess becoming a disillusioned "dirty-something" has sapped my nerd potential. I'm telling you young punks - ten years ago I would have aced this test! Hah!

Nah, not really.

Story of A Biotechnopreneur

You might be thinking: "For a Singaporean biogeek you seem to only write about American computergeeks."

Well, I admit that there's been a bit of an availability bias so far.

But it's all OK now - Fresh Brainz brings you the exclusive story of a Singaporean Biotechnopreneur!

Yes "biotechnopreneur" is one whole word. I'm a fan of German.

Mopsgeschwindigkeit!

Anyway, back on topic.

This is a story about Dr. Rosemary Tan, founder and CEO of Genecet Biotech and Veredus Labs, based on her lecture on 4th Sept 2006.

Born to an upper middle-class family, Rosemary wanted to be an air stewardess as a kid, but her parents wanted her to be a medical doctor.

When she went to the University of Calgary in Canada, she initially enrolled into pre-Med, but in the third year she decided not to continue. Instead, she volunteered to work as an unpaid technician in a biology lab, eventually graduating with a degree in molecular biology.

After her bachelor's she went to Osaka University in Japan on a government (EDB) scholarship to pursue her twin interests in biology and Japanese.

She was the only girl in class. Her first three months adapting to life in Japan was so difficult, that it helped to build her determination to succeed. When an opportunity arose to enroll in the prestigious University of Tokyo, she did a 5-hour entrance exam completely in Japanese, just like a Japanese applicant.

And she was accepted!

After her studies in Japan, she returned to Singapore where she finished her PhD at the National University in a frenzied two-and-a-half years. She wanted badly to be independent and create her own ideas, but a one-year stint at the National Cancer Centre made her realize that, as a young researcher, she had to be realistic.

Rosemary was very impatient and decided not to continue her postdoc. Her dream was to start a company.

But what sort of company would that be? She worked briefly for a consulting firm and discovered a market need - education! At the turn of the century, the Singapore government had just embarked on the Life Sciences program for secondary schools. She used her own savings to start a company, Genecet Biotech, which would concentrate on providing educational molecular biology kits to schools.

From a simple beginning in a small factory space with 2 staff members, Genecet grew from strength to strength. It diversified from making educational kits to making educational card games and other products. In four years it had grown to incorporate its own lab and was involved in 70 programmes.

Rosemary always targets the top schools for her initial product release because she knows that they are trendsetters. All the other schools will simply follow (that happens a lot in Singapore *wink*).

With the success of Genecet she set her sights on a higher goal. A medical diagnostics company called Veredus Labs.

After fending off a number of challenges from powerful competitors, Veredus has found a niche selling field-usable diagnostic kits to detect a number of infectious diseases, including the feared H5N1 bird-flu virus. This kit has been tested to be highly accurate by the World Health Organization (WHO) in January 2006.

To continue to produce high quality products, Veredus has collaborations with research institutes that study the basic science behind the disease. It also has its own in-house R&D which is working on future innovations such as the Lab-On-A-Chip technology.

So what are the take-home messages of her experience?

1. Dr. Rosemary Tan's personality

- She wasn't a top student, and has never been exceptional academically.
- In Tokyo she found out the difference between the best scientists and mediocre scientists: the best never take breaks. While in Japan she worked every day and never went for a single movie.
- She is very hardworking, independent and aggressive.

2. Regarding entrepreneurship

- You should start a business based on what your strengths are. For her it was education in biology.
- Your company must make money, it must be sustainable.
- Don't buy everything, you should build slowly and watch the bottom line.
- You should employ capable staff and avoid relying on "friends".
- Rosemary stresses an attitude of extraordinary service.
- You do not go to the same market as your competitors.
- You should look for novel ideas to solve the problem.
- You need reliable partners and collaborators to help you succeed.

3. Should YOU become an entrepreneur?

- Are you willing to risk it all? Entrepreneurship demands all of your time, resources and effort. Rosemary has not gone out for lunch for years.
- Is it worth it? She does not regret becoming an entrepreneur, but as a working mum when she has to leave her kids at home to travel the world, she can't look back or she'll never leave.

In the Q&A session I asked Dr. Tan if her science training was ever a liability to her entrepreneurial work. She said yes and she felt that the scientists are too detailed and too stubborn.

I then asked her what characteristics does the industry look for in a potential employee. She replied that you should be:

- aggressive, eager, willing to learn and apologise for your mistakes.
- able to multitask.
- able to acquire broad-based knowledge.

It is also helpful if you have some experience working in a multinational corporation (MNC).

Before she concluded her talk, Rosemary said only half-jokingly: "Don't be an entrepreneur."

That immediately reminded me of what Jeff Hawkins said in his lecture: "Entrepreneurism is a tool of last resort."

So what do I think?

I think that she is an important person doing important things for this country. I, on the other hand, am an ordinary student who doesn't know how the world works.

Which is why you get to read cool articles like this for free!

Booyah.

Saturday, September 16, 2006

Real Science

Listen up, my friend. Everything that you've learnt in school about science is wrong.

This is the real deal.















It's so punny that eye roughed my pucking hairs loft! :D

Though due to the sheer volume of insider jokes, I believe that its amusement value depends on your level of geekiness.

If you don't get it, then you must either be a rich fuck, or a lawyer.

Go away.

If you find it hilarious, then you're doomed (to the core!) to an underpaid and underappreciated life of geekdom. Oh my, more fresh brainz for the grinder!

MUAHAHAHAHAHAHA!

Here is another book written by this cool dude Tom Weller.

Enjoy!

Friday, September 15, 2006

As Easy As A-B-C

Where Not To Park Your Car

One day, if you suddenly find a gaping hole on the roof of your car, this is the reason why:




Looks as painful as it sounds :D

Thursday, September 14, 2006

Twigs

Guess what's growing out of people's computers nowadays?





Come on, make a guess first before you scroll down.


















These.

Oh well, I think these are those kind of gizmos that looks cool for the first few days you own it - and then quickly becomes an utter inconvenience for the rest of its functional life.

Just imagine popping one of the spikey ones into your pocket and walking around with it.

Ow Ow Ow Ow.

Not funny.

Guys, you can really ruin your "future" (Chinese 前途) with one of these ;)

Wednesday, September 13, 2006

Perfectionist Procrastinator

Just a few days back I was talking about Steve Jobs, the uber-salesman and perfectionist. Turns out that he isn't only picky about product details, he is picky about everything!

Here is an article about how he became really upset when Pixar went public.

Because there was no carrot juice.

Of course, Steve has his legendary energy to drive him towards completing his tasks. What about other perfectionists who procrastinate because they absolutely cannot stand imperfection?

Actually that seems to be a common problem. To quote Voltaire:

The perfect is the enemy of the good.

Obsession with perfection is a common feature of high-achievers, but the flip side of that same coin is this compulsion may result in delay after delay. Or projects that are never completed.

Or even work that never gets started.

Here are some interesting articles describing the perfectionist attitude and how it can result in procrastination. I have pulled out one useful quote per article, in case you have no time to read them all.

1) In technology...

Making Good Technology Choices

"The greater the push for the perfect plan or result, the more chance what we will instead find is delay."

The Perfect is the Enemy of the Good

"If a company is overfocused on process at the expense of getting to market, I guarantee that it will be climbing uphill against companies that place more emphasis on speed to market."

2) ...and in medicine.

Perfect Is the Enemy of the Good

"The problem is when perfect, being the enemy of the good, freezes us into inaction... Quality improvement is not about a single, billion-dollar fix. It is about a billion one-dollar changes."

Perfect is the enemy of good

"All along I should have realized that trying to do the perfect job—prolonging the operating time, and exposing the intra-abdominal organs to further trauma—would not have saved this patient's life and could in fact have been dangerous."

As for me, I was once quite the perfectionist myself. Grandiose plans never put into practice! Now though, as I grow older I become less picky about the details.

I think it's got to do with my general lack of caring.

Anyway, if you have procrastination issues, Steve Pavlina has written a very good article on how to deal with it.

Overcoming Procrastination

"The solution to perfectionism is to give yourself permission to be human... Realize that an imperfect job completed today is always superior to the perfect job delayed indefinitely."

Wise words my friends. So in future if I ever get criticized about how sucky Fresh Brainz looks, I'll just point them to this post.*

Muahahahahaha!


*Actually this post was edited at least three times before it was posted. At Fresh Brainz quality control is important, but our commitment to daily updates is also important!

Tuesday, September 12, 2006