The 8 Million Dollar Shark

Last Thursday, a research group in Singapore has successfully obtained US$5 million (S$7.7 million) from the US National Institutes of Health (NIH) to sequence the DNA of the Elephant Shark.

This is a collaborative effort between the Institute of Cell and Molecular Biology (IMCB) in Singapore and the J. Craig Venter Institute in the USA.

Associate Professor Byrappa Venkatesh is the principal investigator of the Singapore team. They spent more than two years searching the world for a suitable shark species.

The project is already well underway and Prof. Venkatesh estimates that it will take up to two years to complete.

You might be thinking: "Almost 8 million dollars for a shark genome? WHY???"

Is it a particularly pretty shark?













Heh, not really. With funny looking teeth, buggy eyes and an ugly snout, the elephant shark is not much in the looks department.

Just compare it to the graceful curves of an elegant blue shark below.












What a striking contrast!

The Straits Times reported that the purpose of the project is to learn more about gene function and improve our understanding of human diseases.

That is the long-term goal of many genome projects but not the main reason why this bizarre-looking shark species was chosen. There were no details about the evolutionary significance of this project.

It was also inaccurately reported that sharks were the first creatures to develop nervous and immune systems (invertebrates eg. insects already have those, just that sharks have immune systems that are relatively closer to humans).

Not many fun details from a newpaper report!

So, based on a lecture given by Prof. Venkatesh in January 2007, Fresh Brainz is delighted to answer the biggest question on your mind:

What's so frickin' important about this ugly shark?

1. Outgroup Species To Study Fast Teleost Evolution

This may sound strange, but fish are the largest group of vertebrates. There are over 28 000 species of fish, of which about 27 500 are ray-finned fish. In comparison, all the other vertebrates (including human beings) combined add up to only about 24 000 species.















Ray-finned fish are interesting to scientists because they have evolved a wide variety of shapes and sizes. This is especially true for an infraclass of ray-finned fish called teleost fish. This rapid diversification of body forms is called the teleost radiation.

How did the teleosts evolve so quickly?

One possibility is because of a whole genome duplication event that happened approximately 350 million years ago. Teleost fish have duplicate copies of many genes compared to other fishes, and even mammals such as us.

For example, mammals have 4 sets of Hox genes, whereas teleost fish have 7 sets (2X4 sets with one set loss). This increase in genomic information may have provided the raw materials for fast teleost evolution.

Scientists already have genomic information from teleost fishes such as the zebrafish and fugu, but in order to discover teleost-specific features they need an outgroup species for comparison.

Cartilaginous fish, such as sharks, are good candidates as outgroup species because they occupy an appropriate position on the evolutionary tree.

Also, sharks don't appear to have undergone a genome duplication event. In fact, sharks evolve so slowly that their DNA substitution rate is 7 times slower than other fish. This may be one main reason why sharks appear relatively unchanged for hundreds of millions of years.

2. Smallest Shark Genome

OK, so it's important to go get some shark sequence. But which shark should it be?

Unfortunately, preliminary data showed that the genome sizes of well-known sharks tend to be much larger than the genomes of human beings. This means that the sequencing effort would involve a lot of time and money.

So Prof. Venkatesh and his colleagues searched the globe for any rare shark species that has a more compact genome. Eventually they tested the elephant shark (Callorhinchus milii) which is native to the waters of south Australia and New Zealand.

Early estimates of its genome size was about 1.2 billion base pairs of DNA (compared to human 3.2 billion bp). Later as the sequencing work progressed this figure was revised to only 910 million bp, the smallest genome of any known shark.

This made the elephant shark the most attractive shark model available.

3. Surprisingly Similar Genomic Structure To Humans

Although sharks are more distantly related to humans than teleosts, sequencing results revealed that they have a surprisingly closer genome structure to us.

This was discovered by comparing regions of synteny between sharks and humans. If a particular set of genes had exactly the same arrangement in both sharks and humans, then that region is called a syntenic region.

Current data indicates that syntenic regions are more conserved between humans-and-sharks, compared to between humans-and-teleosts.

Thus, the elephant shark genome project is a useful resource for the detailed investigation of human genomics. It can also be used to study the genomes of many other vertebrate animals.

Not too shabby for such an ugly shark.

Not too shabby.


Would you like to know more?

- Elephant shark genome project website
- Choosing an appropriate model organism

Tree Of Life Art

In October last year there was a competition for a creative project that combined Art and Science in Singapore. I submitted a proposal for a light sculpture called the Tree of Life, which would display phylogenetic data in a physical form that is accessible to the public and fun to play with.












The Tree of Life would have fibre optic "leaves" that can change colour to trace evolutionary relationships between well-known organisms. It would also include a display screen to allow database searches and display interesting facts and videos about highlighted organisms.

The proposal was rejected in the second round of selection, but I still think it's a pretty tree. Click on the above picture for the full-size artwork.

It should have a place right here on Fresh Brainz together with my random art and obscure cartoons!











I went through a number of designs to find the most attractive one. Here's a pen sketch of the finalized form of the tree.









The inspiration for the physical Tree of Life came from the Tree of Life Web Project, which is an excellent resource for phylogenetic information and photos of many living organisms.

Do check it out!


Would you like to know more?

- Tree of Life Web Project

March Of The Giant Penguins!

Palaeontologists from the North Carolina State University have discovered fossils of giant penguins, not in the icy plains of Antarctica, but in the deserts of Peru.

One newly discovered species is Icadyptes salasi, which stood 1.5 metres tall and lived over 35 million years ago.









Here is a picture of its skull compared to a modern Peruvian penguin. The I. salasi had a beak that is so long (30 cm) that experts believed that it might have been used for spear fishing.

With this discovery, Fresh Brainz is proud to bring you the latest update to penguin evolutionary history.

Revealing astounding new relationships never before imagined!

















Somehow, you always knew.

Heh.


Would you like to know more:

- News release about this discovery by Dr. Julia Clarke's group

Naysayers Strike Back!

Science policy analyst Cong Cao, who worked in Singapore before, wrote a letter to Science magazine (8 June 2007), listing a number of challenges that the Singaporean scientific endeavour faces.

And it quickly drew a response from a world-renowned Singaporean, who agreed wholeheartedly with the article.

At Fresh Brainz we spare no effort at the critical examination of criticisms.

So here is a blow-by-blow analysis of the key challenges that Cong Cao described:

1. First, biotech research is uncertain and it can take many years to achieve a breakthrough. Furthermore, advances in understanding pathways operating in human beings are not automatically translatable into commercialized, profitable products. It is not unusual for a pharmaceutical company to spend 10 years and billions of dollars developing a new drug. Although improvements in drug-screening technologies, automation of the screening process, and advances in genomics may change the “hit-or-miss” drug discovery process and shorten the development cycle, pharmaceutical companies will continue to see high rates of failure and enormous development costs. It remains to be seen whether Singaporeans are ready to embrace uncertainties and tolerate failures.

Research is uncertain, that is true. However it is not necessary to have a "breakthrough" in order to reap commercial benefits from research. Inclemental improvements, whether driven by basic science or technology R&D, can have good potential for profits - this depends on many market-related factors.

Ironically, Dr. Cao shows us that he is already aware of this, by pointing out two such improvements (drug-screening technologies and advances in genomics) that can help pharma companies streamline their drug development process - two key areas in Singaporean biomedical research today.

As for the high rate of failure in pharma companies, I should clarify that while there is a high failure rate for pharm start-ups, established international pharma companies continue to generate strong sustainable revenue. Thus they are a good starting point for collaborations.

Still, I share Dr. Cao's concern about how a new generation of Singaporean biotech and pharma start-ups will fare in the face of uncertainty, failure and intense international competition (see point 2 for more details). Currently, only a handful of Singaporean start-ups are sustainable operations.

I should mention that Dr. Cao's use of the buzzword "breakthrough" and use of "biotech" when referring to products to be used directly in people (should be "biomed") are clues that tell us that his primary training is likely not in science.

2. Second, the talent challenge may not be easily resolved. Singapore has started using a government fellowship program to send students abroad. But it will take at least 10 years—the normal time for a doctoral degree plus postdoctoral research experience—for them to become independent researchers and longer to become internationally renowned. Also, in contrast to the United States, where the biotech industry has benefited from strong entrepreneurial efforts by academic scientists, their counterparts in Singapore, as civil servants, operate in
a highly rigid, hierarchical system where moves between academia and industry are rare. Also, Singaporean youngsters may not be willing to stick to tedious benchwork that may or may not lead to financial rewards.

The timeframe is incorrect - the pioneer batch of A*Star PhD students will be graduating this year. If we use Dr. Cao's assumption that they will need to undergo two postdocs (usually 2 X 3 years), then it will only take 6 years before they return as independent researchers.

Even the students who entered the Life Sciences program after the announcement of our biomedical initiative (2002) will be ready in 8 years' time, likely sooner.

However, Dr. Cao is right that they will take much longer to become internationally renowned scientists. I know of three students in the my field of research who I think have the potential to become world-leading scientists.

Of course most students won't get there, but that's also true of any group of students, even in the USA.

It will be helpful, but not necessary to produce many world-leading scientists in order to have a sustainable biomedical research and manufacturing endeavour. Large pharma or biotech companies rarely have renowned scientists (excluding their advisory boards). It is, however, crucial to have a sizeable number of well-trained scientists and technical staff.

As for the tradition of close links between entrepreneurs and academics in the United States, I agree that Dr. Cao has a good point. It's tough for a good scientist to also become a good entrepreneur; I personally feel that the training to become a scientist almost runs opposite to entrepreneurship.

I don't know what the government expects of A*Star students, but if the plan is for many of them to start companies, then I think we have a real problem. Entrepreneurial training needs to begin early. In fact, if they successfully become world-leading scientists with strong personalities then it will be very difficult to switch them towards the entrepreneurial mindset.

Until the time when an entrepreneurial tradition in science becomes established here, there will be a strong demand for people who have the difficult job of acting as intermediates between scientists and the business community.

3. Finally, research in Singapore profited from the ethical debates that mired stem cell and cloning research in the United States. Less restrictive rules may have been an inducement to some foreign biotech companies to set up operations in Singapore. Of course, that does not mean Singapore has no regulatory framework to review research and enforce any recommended ethical code. But Singapore’s advantage may not last if the research environment becomes more open in other countries.

It's hard to say how much Singapore has benefited specifically from the stem cell controversy in the USA, since other research powerhouses such as the UK have had open research environments for years. Nevertheless we are attracting a significant number of world-leading scientists, as well as new pharma investments to our tiny island.

There are many reasons why this is so, including an attractive tax structure, intellectual property protection and an educated workforce. In order to become more attractive than Singapore for research and manufacturing, a competing nation will need to address all these factors, in addition to having a more open research environment.

I agree that we cannot tell for sure how long Singapore's advantage will last.

But if what Dr. Cao really means is that the United States will quickly catch up in embryonic stem cell research once the political pressures ease after 2008, then I only have one thing to say:

You're too late.

It's not Singapore you have to worry about. Even if all political opposition to stem cell research evaporated today in the USA (which realistically won't happen for years) - Japanese and British research groups have gone so far ahead that you will need a long, long time to catch up.

4. More importantly, there should be better opportunities for civil society in Singapore to debate the issues related to biotech research. Citizens have the right to know much more about the risks and benefits associated with the biomedical sciences conducted in Singapore than they do now. Public understanding is at least as important as deep pockets and a deep talent pool.

If I am reading this correctly, Dr. Cao wonders why there isn't widespread debate about biomedical issues here, unlike the explosive and divisive situation in the United States.

He thinks cynically that it's because there is insufficient public information regarding bioethics.

Well, I can be even more cynical than that.

It's not that public information on bioethics isn't available, you can read about it anywhere: in the newspapers, on the Internet, there are even public talks on bioethics.

The real reason why most Singaporeans don't fight over ethics in science is because - they simply don't care about science at all.

Scientific culture doesn't exist among the general public. This is hardly surprising considering that even our oldest biomedical research institute is only 20 years old.

This is also why there are only 2 science blogs in Singapore, out of a few hundred thousand blogs. In contrast, there are hundreds of political blogs read by thousands of Singaporeans daily.

Heh.

To sum up: A number of informative criticisms about Singaporean science, which I have addressed in this article, have been raised by Cong Cao.

Is he a pessimist? Not quite.

Let me point out that, in stark contrast to this letter, he had a glowing appraisal of China's R&D efforts while working in Singapore.

He is now working in the United States.

Also interesting to note that a critical view of his letter accepted it without any criticism.

I know that naysaying can be fun, but like James Bond says - "It wouldn't do to make a habit of it."


Would you like to know more?

A review of Cong Cao's book
- China's Scientific Elite

Don't Shoot The Puppy

Aww! What a cute puppy!

Look at its cute floppy ears and cute little tongue!

So cute! SO CUTE ♥♥♥!












*BOOM!*

YOU BASTARDS! HOW COULD YOU SHOOT THE CUTE PUPPY!

HOW CAN? HOW CAN!?!!

Relax, this is yet another satirical joke pretending to be a flash game.

Click the picture to play.

It doesn't make sense at first, but after passing a few levels you will get the point.

Sometimes the hardest thing to do is not to do anything at all.

Just like in Life!

Heh.


Would you like to know more?

- The Impossible Quiz

Real Virtuality Part III

After Plato, another philosopher's idea was to become a major setback to the development of modern scientific thinking.

In the mid-17th century, French philosopher René Descartes proposed an idea called Dualism.

To explain it simply: Descartes believed that the body is like a machine that follows the laws of physics, whereas the mind (or soul) is non-material and does not follow the laws of physics.























The pineal gland links the physical body with the non-material soul.

Since the soul does not exist in the physical Universe, it can only be examined via supernatural methods.

On the good side, Duality officially allowed scientific studies on the body (which before Descartes' time was considered to be sacred and cannot be dissected), leading to important discoveries that tell us how our bodies work.

On the bad side, it helped to discourage scientific studies into the human mind for about two hundred years.

Things only started to improve towards the end of the 19th century, with the rise of the new science of psychology.

One early idea in psychology that is important to this real-virtual discussion is the concept of Gestalt. This can be summarized as "the whole is greater than the sum of its parts".

Gestalt psychologists observed that we don't always arrive at the overall meaning of something by looking at its components one by one.















Just like how this dog suddenly appears out of the background noise of black blobs - sometimes we see the meaning all at once, as a whole.

New properties that cannot be predicted by studying the components alone are called emergent properties. Emergent properties tend to be processes rather than physical things.

Gestalt psychologists described this phenomenon of emergence, but they could not explain it.

Enter systems biology.

In the 1960s, Austrian-born biologist Ludwig von Bertalanffy wrote General Systems Theory, where he proposed that living organisms are complex, open systems.

Unlike a simple system, where you can learn about its overall properties by studying each component in detail, a complex system does not have additive, easily predicted properties.

This is because a complex system has many strong, non-linear interactions between its components. Many of these components are organized in feedback and feedforward loops that affect the function of other components.

A complex system often has multiple levels of organization, each level regulating the activity of lower organization levels and becoming a component of a higher organization level.

Higher organization levels can have emergent properties which are meaningless at lower levels.

In addition, living organisms are also open systems, which means that they are constantly interacting with the external environment. So the emergent properties of organisms also depend on where they situated.

Thus the overall explanation is:

The "mind" is what the brain does, like "spell" is what a school kid does.

You cannot find a "spell" in the cells of a person, but without cells there can be no "spell".

Similarly you cannot find an Internet in a computer chip, but without computer chips there can be no Internet.

Complex systems have emergent, "virtual" functions that feel far more real than the physical components that make it.

And in the case of multiplayer online games, the computer's virtual reality can become so real and so attractive that some people have become hopelessly addicted to it.

Trading one virtual reality for another.

To the extent that they could neglect their physical lives and even kill themselves.

Online games, the entertainment industry, alternative medicine practitioners and motivational speakers all try to sell a "virtual" world that appears more real, more ideal, and more wonderful than physical reality.

It's hardly surprising that they are so popular.

Even I find the world of video games incredibly engaging.

Heh.

Unfortunately, the truth remains...

When somebody dies, so does the person on the other side of the mirror.


Would you like to know more?

- What is Systems Theory?

Real Virtuality Part II

Plato was an ancient Greek philosopher who wrote The Republic, a book of philosophical ideas and political theories.

One main idea in his book was the Allegory of the Cave.












To explain this allegory simply, Plato believed that physical objects are not real.

They are analogous to the shadows of puppets that are cast on a wall, projected by a bright light.

The real causes of the shadows are the Forms (the actual puppets). Forms are Perfect and Eternal things. One quality they have in common is the Form of the Good (the bright light).

He believed that you cannot understand the essence of reality by studying the shadows, since shadows are temporary and unimportant things.

The only way to reach the truth is by reflection and divine contemplation.

Thus, it is pointless to study Nature by observations and performing experiments, since all you can learn will be meaningless details about "shadows".

Because Plato was such a influential philosopher, his ideas became the basis of spiritualistic worldviews that was to gain a strong foothold on social and political systems, even till today.

And helped to impede the progress of science for hundreds of years.

Heh.


















Plato (left) points to the Heavens while Aristotle (right) points to the Earth.

Lucky for us then that Aristotle came along. This wayward student of Plato was so opposed to some of his master's teachings that he was not appointed the head of Plato's Academy.

Instead of Eternal Forms, Aristotle believed that the ultimate reality is found in physical objects, and can be discovered by experience.

He had many interests - anatomy, astronomy, economics, embryology, geography, geology, meteorology, physics and zoology - and he studied these subjects by direct observations of Nature. Today we call this an empirical approach.

Though Aristotle had other wacky ideas and made some errors, his approach is much closer to the practice of modern science.

You're thinking: "Two dead philosophers. What's this got to do with the human predilection for virtual things?"

Well, it turns out that Plato might have a twisted idea of what constitutes reality, but his observation is partially correct.

Physical objects are real, of course, but the concept of "realness" doesn't exist unless you have a conscious mind to interprete them as such.

And for all his contributions to modern scientific thinking, Aristotle's assertion that the ultimate reality is in physical objects is partially wrong.

The "real" world we sense around us is actually a process produced by the interaction between our bodies and the physical world.

Our minds are already a type of virtual reality.

The mind is NOT merely an illusion. It feels so real that for centuries many people believed that the mind (or soul) exists in some transcendental realm, separate from our physical bodies.

We know this to be false because individuals with brain injury, or under the influence of certain drugs, or under situations of extreme stress and fatigue, perceive their world very differently from other people.

Humans tend to favour virtual things, because Life itself is a process - a real virtuality.

So, how did I arrive at this conclusion?

Stay tuned for Part III ("Emergence" of Gestalt and systems biology!) ...

Real Virtuality Part I

Which one of these is a real image?

1. A photograph of you
2. Your reflection in a mirror

You are thinking: "HAH! That's simple secondary school physics. The photo is a REAL image. The reflection is a VIRTUAL image. Who doesn't know that?"

Yes, you're right.

But which image feels more real?

I mean, just look into a mirror.

It's YOU right there!

She moves! She breathes!

The "person in the mirror" feels so real that it is a common theme in numerous fantasy and horror stories.

Never mind the fact that it is merely a virtual image, a transient stream of photons that disappears the moment you walk away from the mirror. You can't hold it in your hand or keep it in your pocket.

What about a photograph then?

Well, a photo does have more permanence. It is printed on a physical medium, and you can store it for years.

So you can laugh at your nerdy fashion sense or cry at your loss of youthful beauty ten years down the road.

But even the highest resolution, most artfully taken photograph is still flat and lifeless compared to your image in a mirror.

It's a real image, but it doesn't feel as real as a virtual image.

Why?

And more importantly, why should ANYONE care???

Heh, I'll give you the straight goods.

$$$$














Fact: The MMOG (Massively Multiplayer Online Game) global market size has hit US$1 billion in 2006. Role-playing games such as World of Warcraft and virtual worlds such as Second Life are so popular that the market is projected to reach US$1.5 billion by 2011. Second Life may be a virtual world, but it has a real economy: nearly US$1.6 million dollars are traded daily within the game.

Fact: Actors who play doctors on TV earn more money than real doctors. Noah Wyle, who played Dr. John Carter on the TV show ER, earned an estimated US$9 million in 2004 - a staggering 45 times more than the average salary of actual ER doctors. As for actors who play doctors in the movies... let's not even go there.

Fact: "Alternative" medical practitioners can also make more money than real doctors. The US market for complementary and alternative medicine reached US$5 billion in 2005 and continues to grow. CDC reports that a whopping 74.6% of Americans used alternative medicine in 2005. Hugely popular products and services - which have little or no therapeutic effect when tested scientifically.

Fact: Motivational speakers and trainers make a tonne of money. In 2006, the total US market for "self-improvement" products and services climbed to US$9.6 billion. One example is the popular motivational speaker Deepak Chopra who often passes off diffuse and mangled nonsense as deep wisdom.

And...

Fact: The biggest personal fortune ever made in human history was built on the foundations of a "virtual" concept - software licensing. Bill Gates didn't make his billions of dollars building computers. He didn't even write the original code for the first MS-DOS. But yet he took only 30 years to amass a personal wealth of US$56 billion. In comparison it took Coca Cola more than one hundred years to reach a total worth of US$58 billion.

Now - do you see the importance of examining our peculiar human tendency to regard virtual things as more real than real?

Some kind of "Real Virtuality", if you will.

It makes cents, of course.

But it also makes sense.

Stay tuned for Part II (It's all Plato's fault!) ...

A Dead Horse And A Hot Babe

Only at Fresh Brainz will you find a photo of a dead horse next to hot babe.

Heh.

Of course you are asking: WHY???










Exhibit A: The skeleton of Eclipse, an 18th-century champion racehorse which was never beaten on the racetracks.

Exhibit B: Charlize Theron, uber hot babe and accomplished character actress.

Turns out that they have something very important in common.

They are both "average" individuals.

OK now you are going: WTF!?!!

Relax, I'm going to make this crystal clear in just a minute.

But first - a nice, big mystery for you.

If the hottest babes in the world are so rare, then why do so many people find them beautiful?

I mean stars couldn't become "stars" if only five people in the world thought they looked awesome, right?

It's true that people who look like Charlize Theron, Aishwarya Rai or Ayumi Hamasaki are hard to find. But so are people who are 90cm tall or people who weigh 500kg. Yet very few people would find such unique individuals attractive.

"Uniqueness" appears to be a popular catchphrase in society. There is a powerful, innate drive in human beings to distinguish ourselves from the crowd.

Yet despite the heroic efforts that people use to differentiate themselves from the thronging masses, little did they realize that nobody actually lives in Average Land.

It's like the place where the curve y = 1/x meets the y-axis or the point where parallel lines meet.

It doesn't exist.

There really isn't an average person who is 1.71m tall, earns $25 150.43 a year, drives 1.3 cars, keeps 0.7 cats and has 2.1 kids.

Maybe except in Novaya Zemlya.

The faceless average person is just a mental concept that we use to simplify the world and to separate the "me" from everyone else.

In reality, everyone is unique. We are all decidedly non-average in some physical or mental attribute.

Uniqueness is not something to aspire to - it's something you already are.

And it isn't something necessarily appealing neither. It's just... different.

As a matter of fact, when it comes to physical attractiveness, psychologists have proposed for a number of years that the "averaged" face is the most beautiful for most people.

An "averaged" face is a computer-generated model that morphs the average facial dimensions of a number of people into a single image.

Instead of becoming increasingly ho-hum as more faces are added into the database, the generated model actually becomes increasingly beautiful!

People with facial proportions nearer to that of an "averaged" face are considered attractive by far more people than people with "unique" faces.

More of a mass market appeal, as business types would say.

That's fine and dandy, but what's all this got to do with an undefeated racehorse?

Well, scientists want to find out what makes a champion racehorse gallop so fast.

So, they modelled Eclipse's skeleton on a computer and analyzed the movements of its reconstructed limbs.

Did Eclipse possess some incredible anatomical features that explained its speed?

Ultra-long, ultra-strong legs?

To their surprise, they discovered that Eclipse was average in almost every feature. Yet the combined effect of all these attributes resulted in a very speedy horse.

I know it sounds tad bizarre, but perhaps deep inside everyone really prefers to be "average", because that is the impossible ideal.


Would you like to know more?

- Psychology of facial attractiveness
- Why was the racehorse Eclipse so good?

Four Buzzwords I Hate

What's that annoying buzzing sound that's flying around my head these days?

Is it mosquito?

Is it an electronic mosquito repellent?

Or is it the last, gasping hiss of the remains of an electronic mosquito repellant after I twack it repeatedly with a rubber chicken?

(It's supposed to be "ultrasonic", so why can I still hear its teeth-grinding, high-pitched shriek? WHY???)

No.

Fresh Brainz is deliriously happy to bring you the worst of the worst - Four Buzzwords That I Hate:

4. World-class

Singapore has many world-class features: a world-class airport, world-class convention centre, world-class art centre, world-class education system and world-class transport system.

But has anyone stopped to ask: where exactly is this place called "world"?

This magical place where there are four million smiles and perfectly pristine public toilets?

Is it in Reykjavik?

And why is "world-class" so similar in practice to "by American standards"?

If it actually means "by American standards", does it mean that we should aspire to have the calibre of their soccer teams, the artistic quality of their inner city graffiti, their unhindered freedom to walk around with automatic weapons, and the state of their current science education?

It if really means "by European standards", shouldn't we aim to build an endless stretch of nude beaches, open bakeries enhanced with all sorts of mind-expanding drugs, and manufacture cars that stop running once the temperature climbs above 30 degrees?

Wherever the "world" is, everyone wants to live there.

3. Bicultural

"Culture" is an easily misused word, since it has so many meanings. In biology for example, culture usually means the growth of bacteria or cells.

In daily usage, culture has two common meanings:

a. A high degree of taste and refinement formed by aesthetic and intellectual training.

b. These patterns, traits, and products considered as the expression of a particular period, class, community, or population.

Here in Singapore, at the intersection of the East and the West, a mysterious new buzzword has emerged to describe people who embody the best of both "worlds" (see above).

Bicultural.

Wait a sec.

If we are talking about the development of aesthetic taste in an individual, how can one person have two cultures - unless he is suffering from a split-personality disorder?

If we refer to the prevailing customs of the local population in Singapore, how can one person have two cultures in one country?

To matters worse, the exalted title of "bicultural" has been given to people who were born in some country, educated in another, just stepped into Singapore for two days... and suddenly they are bicultural Singaporeans!

They haven't even learnt how to order a dinosaur with extra Milo powder yet.

Oh my.

For me though, it's simple. Singapore may be strongly influenced by both the East and the West, but as a Singaporean, I only have one culture - Singaporean culture.

"Monocultural", if you like.

2. Self-radicalization

Comedian George Carlin once had this criticism for another ubiquitous buzzword "self-help":

If you could do it yourself... you didn't need help!

A similar problem here with the term "self-radicalization". Individuals who sought out extremist websites on the internet were not "self-radicalizing".

They were radicalized by somebody else. Through the internet.

Unless... they set up the websites themselves.

1. Passion

And the Ultimate buzzword that makes me throw up is - PASSION!

It's used so often and thrown around so indiscriminately that it has become a horrible cliché.

Passion at work... passion for science... passion for entrepreneurship... passion for success... passion passion passion...

Enough!!!

The biggest problem with this concept of passion - it is always after the fact.

If a person becomes successful, then she was "passionate" about her work.

If she failed, then she was obsessed. Or fanatical. Or obstinate. Or reckless.

Or even "not passionate enough" - whatever that means.

The language used to describe their efforts becomes completely opposite. Business analysts have observed this psychological bias for years.

Thus, I've decided that for me there are only two legit uses for the word "passion":

a. A type of fruit.

b. A hot night of wild lovin'.

Man do I have language issues this week.

Heh.

Any other buzzwords that get on your nerves?


Would you like to know more?

About misunderstood and abused words:
- Most Misunderstood Terms In Biology
- Most Abused Catchphrases In Science

About a nice, warm place where buzzwords deserve to go:
- Buzzword Hell

Photo Gallery Two

Fresh Brainz is proud to bring you yet another collection of my favourite original photos.

Now with an even more whimsical edge!

Heh.












Escher's escalators
(2007) Sony DSC-S600
















Evening lanterns
(2007) Sony DSC-S600
















Jaws of death
(2007) Sony DSC-S600
















Lightning strike
(2005) Yashica Electro 35 CC











Party of five
(2007) Sony DSC-S600
















Pink streaks
(2007) Sony DSC-S600
















Steel frame
(2007) Sony DSC-S600
















Tunnel light II
(2007) Sony DSC-S600
















Ultraviolet
(2007) Sony DSC-S600
















Very old friends
(2007) Sony DSC-S600














What lies beneath
(2007) Sony DSC-S600


Would you like to know more?

About other photo collections:
- Fresh Brainz Photo Gallery One
- Sentient Puppets Photoblog

About the cameras I use:
- Sony DSC-S600 (6MP digital)
- Yashica Electro 35 CC (35mm-film rangefinder)

These photos are copyright © 2007 http://freshbrainz.blogspot.com

Rise Of The Silver Squiggle*

Some of you may have noticed something new in the header picture - what's up with that squiggly thing that looks like a mirror image of a question mark?

A good question!

That, my friends, is the shiny new logo for Fresh Brainz.

And there is an actual legend behind its birth.

Make that two legends.

















Fig 1. GFP-expressing D40X cells (100X magnification)

Apocryphal: I was attempting a transient transfection of the D40X cell line using an overexpression vector that I made. It is a Cyan-C / Ju-C fusion protein coupled to an IRES driving EGFP expression as the readout. When I lipofected the plasmid into a 10-cm tissue culture dish of D40X cells, the GFP expression pattern (see Fig 1) was so distinctive that I decided to use it as my blog logo.

Actual: I spent almost a year tinkering with a logo design that either looks like the letter "F", resembles a question mark or outlines the silhouette of a human brain. This silver squiggle just barely manages to do all three.

Yes, the truth is not as spectacular, I know.

*sigh*

Oh before I forget - Fresh Brainz is happy to introduce yet another perky mascot for a new category of posts!
















Paris the Hot Button will be the avatar for future articles about fast-breaking news, socio-political controversies and other current affairs.

And yes, Paris is really named after this weepy young devotchka who is currently doing the old in-out-in.

Jail, that is.


Would you like to know more?

About other Fresh Brainz mascots:
- Fran the Strawberry
- Sally the T.Rex
- Brad the Brain-skull
- Mike the Microphone
- Nick the Camera-robot
- Svetlana the Spacewalker
- Nameless the Blue Question Mark

About Rise of The Silver Surfer:
- Official Website

* Sorry about the pun.

Four "D"s Of Creativity

An avid Fresh Brainz reader* has recommended an article that examines the use of antidepressant drugs (especially Selective Serotonin Reuptake Inhibitors or SSRI) in children.

Unlike adults, the brains of children are still actively developing and thus SSRIs may cause long-term changes to their brain chemistry, resulting in negative effects such as anxiety and increased suicide risk.

Click on this link for more details: Kids on Meds - Trouble Ahead

However, not everyone agrees that the long-term effects are necessarily bad. Some clinicians believe that SSRIs have the potential for more benefits and less side effects in children, compared to adults. More research data is needed to resolve this issue.

In the meantime, experts say that the benefits of SSRIs still outweigh their risks if the diagnosis for childhood depression is made accurately.

I think it is a challenge to diagnose clinical depression accurately. Everyone experiences periods of extreme low sometimes - it is hard to pinpoint whether it is the situation or the person herself/himself who is the major cause of the misery.

Which suddenly reminds me - Fresh Brainz believes that Creativity is driven by these four "D" batteries:

Depression
Despair
Denial
Disillusionment

Happy, contented and well-adjusted people don't create new works of art, invent new technology or discover scientific knowledge and medical cures.

Not at all.

They join the government and become administrators instead.

Heh, that sounds cranky, but it's definitely true.


Would you like to know more?

- Childhood depression
- Antidepressants for children (FDA review)

*Thanks S.R. for this article alert!

Interview With A Post-doc

Fresh Brainz is thrilled to bring you yet another interview with the people behind Singaporean science. This week I am chatting with a post-doc who has a bubbly character and is often cheerful in the lab.

How does she sustain her optimism? Let's go find out!

She prefers not to reveal her identity, so I will call her A*Na for this interview and I've drawn an anime cartoon that is my best representation of her personality.

Heh, I'm not very good at drawing anime.

On with the dialogue!

A*Na: *sees my clipboard containing prepared questions* Wah, so 夸张(exaggerated) ah!

Me: *tee hee* This won't take long. How did you decide to do scientific research?

A*Na: Because I have nothing else to do mah. Just joking lah! My father wanted me to get a PhD. The best option for me is science.

Me: What is your favourite part about doing science?

A*Na: I like to analyze things, I'm the thinking kind. I like to prove my hypothesis correct.

Me: What if your hypothesis is wrong?

A*Na: If wrong, then reformulate the hypothesis lah. I like to plan the experiment and then do it.

Me: What if other people plan the experiments for you?

A*Na: Don't like. If other people plan the experiments then I will not be as enthusiastic.

Me: What do you hate most about doing science?

A*Na: When I do stupid things during my experiment. Because of a stupid mistake.

Me: What about some external factors?

A*Na: I hate it when people keep trying to prove their point.

Me: You mean like confirmation bias? When people selectively fish for evidence?

A*Na: Yes, that's right.

Me: Do you remember your happiest day in science?

A*Na: Oh, there were two actually. When I got my first first-author publication after my PhD. And also when somebody from another group postulated the same hypothesis as me.

Me: What about your most unhappy day?

A*Na: When another group published part of my work during my PhD. At first I felt like giving up, but later I became happy because they showed the same result that I found. This means that my research work is solid.

Me: Which is more important - family or career?

A*Na: Family come first. But luckily my husband is supportive of my career.

Me: Your husband is an endangered species!

A*Na: *laughs*

Me: What is your favourite comfort food?

A*Na: Ice cream. I like Ben & Jerry's ice cream, especially Chubby Hubby.

Me: What flavour is that? I don't eat there...

A*Na: It's caramel with peanut butter and pretzel bits.

Me: What is your favourite chocolate?

A*Na: Belgian chocolate... what you call those?

Me: You mean like praline?

A*Na: Yah, praline.

Me: Is there a fashion accessory that you cannot do without?

A*Na: A watch. I must wear one, usually a digital watch.

Me: To tell the time?

A*Na: Yes.

Me: I mean for a purely fashion purpose. Not for a practical function.

A*Na: Purely fashion? Then it would be earrings.

Me: Is makeup more important or dress more important?

A*Na: Dress is more important for me, because my skin is sensitive. I try to avoid makeup.

Me: OK, last question. What is the most important thing in the world for you?

A*Na: Family ties.

Me: OK, thank you!

A*Na: Can I see the cartoon now?


Would you like to know more?

Other Fresh Brainz interviews:

- Interview with a PhD student
- Interview with a scientist

Only Seven???

Watch this:


















Only SEVEN???

I can't believe the sloppiness of their methodology. I mean, what if the blokes were put off by her coquettish expression?

Or the fact that she is facing them would discourage them from sneaking a peek?

Or the fact that those cheating bastards counted multiple hits for one guy who was obviously turning his head to check out the woman's face?

Such flaky "science".

*slaps forehead*

Sadly, to tell you the honest truth - my straw poll of a few random guys at the lab also confirms their results.

To sum up the sentiments of most guys (clearly excluding me!) :

Boobs = no ogle

Bum = go ogle

Wait... something doesn't sound right.


Would you like to know more?

- More video clips from Brainiac

Fracking Painful Ulcer

I accidentally bit myself last week while stuffing my face with a bowl of fishball noodles.

So now I have a big, fat ulcer that hurts like hell.

Since you didn't ask to see it, here's a big, fat photo of it.

Heh.














It's approximately twice as painful as it looks. Give or take maybe 20%.

Veteran Fresh Brainz readers ("Freshbrainiacz" perhaps?) know that I hate ulcers. I detest them so much I wrote a whole Uncyclopedia article on them.

The problem is that I get them so fracking often. One of our postdocs says that he never gets ulcers. That can only mean that I lack a cogwheel in my head that prevents the teeth from clamping down when other mouth parts are in the way.

Or maybe all the gears are loose anyway.

Speaking of "fracking" suddenly reminds me of fractals: did you notice how my ulcer resembles the Mandelbrot set?




















In the case of my ulcer, the X-axis is facing down towards my finger. It has two round shapes just like the Mandelbrot set picture - the larger wound (cardioid) inflicted by my super-sharp upper right canine.

Well I'm not a mathematician, so I'll leave the detailed explanation of fractals to the professionals.

I'll just comment that the fractal concepts of repeated functions (iteration) and self-similarity are also important to biologists.

One major mystery of biology is: how does a multicellular organism assemble itself during the embryo development process?

A large mammal has to grow from one cell to several trillion cells in a matter of months. This process must be tightly regulated so that the animal forms correctly.

However, mammals only have tens of thousands of genes. One trick to "fold" more complexity into a limited number of genes is to repeat the genetic programming during development.

The same set of genes are used to form both the forelimbs and the hindlimbs. They are then used again in a different orientation to form the digits of the hands and feet. In fact you can consider a finger as a self-similar component of the whole arm. In this way the animal can develop many parts using fewer genes.

Just like the diversity of structures that you can make using a small selection of Lego bricks:















And the myriad ways that I can make my teeth punch through the inside of my mouth.


Dammit.


Would you like to know more?

- How long is the coastline of England?
- Fish with the ancestral genetic program for tetrapod limb formation