Counterintuitive Science: Importance Of Independent Verification

People like people who like them back.

As popular proverbs go: "A friend in need is a friend indeed", or "The best mirror is an old friend".

Wouldn't it be wonderful if everyone you knew became a good friend?

No more hate, negativity, animosity and conflict.

Pure bliss? Not quite.

Actually, if that really happened, you would be utterly fucked.

Why?!??

Two words.

Confirmation. Bias.

You see, there are too many people who think like this:

Human senses are fallible. There are light wavelengths we can't see, sound wavelengths we can't hear, chemicals we can't taste or smell, and even our sense of touch can be highly inaccurate. On top of that, they can become garbled or even deliberately fooled under certain conditions.

Scientists insist on only believing in things that can be physically observed. But what is the basis for this trust in our own senses? Don't you need "faith" to believe that human senses or human logic can actually decipher the true nature of reality?

Since science already takes this leap of "faith", why not abandon our imperfect human senses and use our "hearts" to perceive the ultimate truth instead?

To support this stand, an often repeated claim is that "you can't convince a completely colour-blind person that colour exists."



















Sure you can.

Let the people who claim the existence of "colour" select some distinctly-coloured objects, say "red" and "green" apples, which is indistinguishable to the colour-blind individual.

Then get them to sort the apples by colour.

If different people from different places in the world consistently and repeatedly pick the same specific apples to be "red" and others to be "green", you're on to something.

If animals can also see this distinction, we know that colour is not limited to human senses alone.

If people can demonstrate that different coloured objects consistently reflect a corresponding wavelength of light, which can be perceived and measured by a machine, we know that colour is not limited to living systems alone.

Even better - if a pair of goggles can be made which will represent these colours as different checkerboard patterns, then the colour-blind individual can directly convince herself that colours really exist.

Using such a device, she would be able to sort out all coloured objects, not just apples, in exactly the same way that people who can see colour would.

Of course, this is same principle behind machines like IR goggles or X-ray machines or ultrasonic detectors or carbon monoxide detectors.

Our fallible human senses cannot perceive these stimuli unaided, but no sane person would dismiss their existence.

Let's say that you were tasked to decontaminate a radioactive room. Would you put your trust on a Geiger counter (which was constructed using all too fallible human senses and logic), or would you trust your "heart" that the room is safe?

More importantly, would you base your trust on the Geiger counter on "faith" just because someone in authority told you it works, or would you personally test its accuracy against some known radioactive samples first, before even stepping into the room?

The bottom line is: a single piece of information from one sensory modality is indeed suspect, but if multiple lines of evidence from multiple independent sources all align towards the same result, then the conclusion is highly trustworthy.

This not only forms the basis of science, but also the basis of the criminal justice system for all modern democracies.

In science, this is how we determined that gravity and biological evolution are real phenomena.

In both cases, multiple lines of evidence using numerous experimental techniques, performed by independent (sometimes adversarial) research groups over many years of work consistently converge towards the same conclusion.

No faith is necessary; indeed, disbelief in gravity or biological evolution has no effect on the reality of either process.

However, there is a caveat to this method of gaining knowledge.

The key term is "independent".

You can't trust multiple sources when they are too closely related to one other.

For instance, if my vision and hearing were conveyed into my brain on the same nerve, and I suddenly see and hear something odd at the same time, I cannot count these experiences as two independent sources of information.

That is the reason why there is potential for big trouble if you are completely surrounded by like-minded and mutually-dependent friends who share your ideals and goals.

I'll give you a vivid illustration of this.

Imagine you are an avid mountain climber on your first attempt to conquer Mount Everest. You embark on this arduous journey with a number of good friends all of whom, like you, deeply desire to scale the summit.

Not long after you leave the base camp, you start getting nauseous and tired. Your heart is beating disturbingly fast, and you are beginning to throw up often.

You don't feel so good.

But your friends insist that you are doing fine and that everyone is going through the same difficulties.

Why would they say that? Maybe they have no idea how much pain you are experiencing. Maybe they simply want to encourage you to keep going. Maybe they want you to share the joy of conquering the peak together.

Or maybe you play an important role in the team and they really need you to stick around in order to succeed.

Whatever the case, you reach a camp at the halfway mark with many climbers from other teams. Your friends congratulate you for your efforts.

But a complete stranger notices your physical condition and casually remarks:

"You look like shit. Better turn back now or you'll be the next body count this season."

And then you come across a veteran climber from another team who says:

"Whoa... take it easy, man. I haven't seen another person who is as messed up as you in three years. Maybe you should consider turning back... I know I would."

Who would you trust?

Your friends? Or a couple of unrelated strangers who have nothing to lose or gain from your triumph or demise?

I think you can see that it is unwise to surround yourself with too many friends or yes-men, because they do not represent truly independent sources of information.

Their fates have become too closely intertwined with yours to dare voice out any dissenting views, even if they reflect the reality of the situation.

This may not appear to be an immediate problem for huge social groups which have enough people and resources to craft their own social realities, for example through self-affirmation and self-fulfilling prophesies.

However, cocooned within this semblance of diversity, the group incorrectly assumes that a consensus was reached via multiple independent sources, gradually losing touch with the wider reality.

It may continue to believe that everything is hunky-dory even though many lines of evidence from disinterested parties indicate that major problems lie ahead.

I cannot emphasize enough that conclusions reached using evidence from multiple sources are only trustworthy if the sources are really independent. This strategy serves to compensate for the fallibility of any single mode of information.

You are thinking: "Well, since human senses are imperfect, who cares if it's one human sense or fifty human senses. Why not depend on a single, perfect heart?"

Just a tiny problem there.

Human "hearts" are also imperfect.

If you have ever been heartbroken before, you will know how wrong a "heart" can be.

Bzzzzzzzz!

The Fresh Brainz team is facing immense obstacles right now.

We would like to see the 2nd blogiversary of this little science shack, but this is becoming increasingly impossible.

Hope to be back.

Gone Left Away Passed Departed Exited Egressed

It is with great sadness that we mark the passing of comedic genius and social critic George Carlin, who died of heart failure on Sunday at the age of 71.





















Fresh Brainz salutes this wildly creative, keenly observant and straight talking comedic mind who is a key inspiration for the style of Fresh Brainz itself.

Farewell Frisbeetarian, may you rest on roof.

It's A Trap!

Wow.

Photo Gallery Nine

It's been a while since I've posted the last photo gallery.

Truth be told I haven't had much inspiration for photography lately.

Here are some new-ish evening shots that I've taken, and like I said they aren't particularly great:



















Dragon's spine
(2008) Fuji S6500fd










Reflections from afar
(2008) Nikon L5



















Sky aflame
(2008) Nikon L5









Kallang night
(2008) Fuji S6500fd

Hmm... maybe I need a muse.

Every artist needs a muse who prefers to wear very little clothing.














Muses are yummy.

Would you like to know more?
- Photo Gallery Eight

Touché 2008

Two weeks ago, on the 8th of June, I was invited to speak at the inaugural session of Touché 2008. I gave a talk about the use of the internet for communicating science and introduced the goal of Clearthought Singapore as an avenue to promote rational thinking in Singapore.







During my presentation I emphasized the importance of asking questions as an integral part of the scientific process.

To my delight, the audience raised a number of good questions during the Q&A session. However, I don't think I answered some of them adequately. Clearly I need more practice to think fast and think widely on my feet, practice that rarely comes by when giving routine presentations to a group of bored fellow specialists.

Thus I would like to go over three of the most interesting questions in detail here - two of these are easier to address while the third is a really difficult one.

But first - a quick summary of the event!
















Professional illusionist Nick Sin kicked off the event with his opening performance, inviting the audience to pick one out of five envelopes that contains a $1000 dollar bill.

It's an impressive demonstration that reminds me of a question that I once asked a neuroscience post-doc during my first job:

"If everyone thinks in the same way and chooses the same choice, do we really have free will?"

To which she replied (in a very annoyed tone) ...

"If they can freely choose then they have free will LAH!"

... before resuming her conversation with other lab members about shopping and housing applications.

Over the years I've learnt to accept that basic inquisitiveness is not a requirement for a successful scientific career. Indeed, scientists who hate their jobs or believe in anti-scientific woo will still succeed in their fields as long as they can produce consistent experimental results and publish in good journals.

This reality is far removed from my initial idealism. But I digress.














Dotbox founder / executive director Glenn Goh Cheng Ze and director Serene Yeo gave an animated talk about the key achievements of the social enterprise that they created.

Cheng Ze candidly revealed that his main motivating force is money - resources which he can then use to help make changes in society.

Cheng Ze and Serene were not business graduates - they actually graduated with diplomas in biomedical science, and their accomplishments highlight the fact that motivated and ambitious individuals can forge their own paths to success in spite of difficulties along the way.

It also made me wonder if they ever had an opportunity to try doing scientific research, or were the authorities too busy inviting foreign attachment students into our research labs to give our own students a fighting chance.













The third speaker of the day was Tan Jian Xiong (left in photo), a project director at the Moral Welfare Home. He combined his love of volunteerism and photography to showcase many heart-felt images that he took during some of his overseas community expeditions.

Overall, the event was a great success. Kudos to Touché 2008 chairperson Edgar Kieu (right) and his team for creating an important forum for the discussion of new ideas and social issues.

And now - time to discuss those three questions I was talking about earlier!

1. Does ethics slow down the progress of science?

That depends on what you consider "progress".

If we are talking about the progression of a research project or a field of research, then the answer is yes. The best recent example of this: US government policies limiting their own embryonic stem cell research that has allowed other countries to proceed further in this field.

Science is a societal endeavour and thus scientists can only investigate what society deems acceptable to study. Ethics boards such as the Bioethics Advisory Council in Singapore, in consultation with the public, makes the decision if a particular line of research is acceptable. These organizations consists of professional ethicists, doctors, social experts, lawyers and senior scientists.

On the other hand, if you think of "progress" in science as a matter of increasing benefit to humanity, then it's much harder to say.

To give a positive example, ethical constraints in Europe during the Middle Ages disallowed the dissection of the human body and thus blocked the progression of medical science for hundreds of years.

It was not until the 1500s that mavericks like anatomist Andreas Vesalius forcibly pushed the field forward by engaging in ethically outrageous activities such as snatching the bodies of executed prisoners and performing public dissections - ultimately producing the Fabrica, the first accurate anatomy book in history, which would also help spark off the scientific renaissance.

For a dismal negative example we need to look no further than Second World War-era Japan, when maverick microbiologist Shiro Ishii established the infamous Unit 731 in northern China to study bacteriological warfare. Without any ethical objections to hinder his projects, Ishii tested the use of deadly bio-warfare agents such as the bubonic plague, cholera and anthrax using live human subjects, resulting in the deaths of thousands of Chinese civilians.

From the perspective of the development of bio-weapons it was a resounding success, but in terms of benefit to humanity it was an grevious setback, both in terms of human cost and negative repercussions. Although biological weapons were formally banned in 1972, in the current climate of fear over terrorist attacks, bio-weaponry is an issue that still resonates today.

2. How can scientists of different cultures genuinely cross-pollinate their ideas?

This is possible because of two main reasons.

Firstly, the core aspect of scientific thought - rational inquiry backed up with observable evidence - transcends cultural differences.

The rules of the game are the same.

In addition, the scientific process can discover facts about human beings, for example our perception of beauty, that is cross-culturally relevant. In an international conference, scientists may have a greater emphasis or bias towards the fields that are more valued in their own culture, but they generally accept that rigorously obtained scientific knowledge is true no matter where the research is conducted.

In fact, some scientists consider science itself to be the first form of international "culture" in human history.

Of course there will always be criticisms, valid or not, on the issue of whether science is truly independent of its local cultural context. In the past critics have voiced objections over "Jewish science" or "capitalist science" or "feminist science", today it's still quite common to hear opposition towards "Western science".

To address these criticisms, scientists have to incorporate the necessary controls in their research strategy to rule out cultural biases.

The second reason is that people in general, and not only scientists, can be interested in new ideas generated in other fields and other cultures because there is a unity of knowledge.

Our brains share a common mechanism for gaining, processing and expressing information that allows us to compare the ideas of others with our own ideas and integrate them into our existing framework of knowledge.

3. Is competition or cooperation more important to the progress of science?

This deceptively simple question is really, really difficult to answer.

It is better directed to an established historian of science than to a struggling grad student, but I'll do my best to address it.

It is trivial to state that both competition and cooperation are crucial to the scientific endeavour.

Without cooperation, research groups will fall apart as individual researchers withhold common reagents or critical information from each other and engage in petty politics with their colleagues. Cooperation is gradually becoming more important nowadays as scientific projects become bigger and require large amounts of manpower and expensive resources.

Without competition, project progression may be slow since researchers will think that their line of research is not hotly-contested and thus the novelty of their work is not at risk. In addition, for some scientists, personal rivalry adds a strong emotional motivating force towards defeating their academic opponents using ingenious strategies or pure-dogged hard work. Having no competitors at all would dull their performance.

I would say that competitions in science, especially feuds involving two prominent scientists of similar stature, is highly over-represented in the popular culture, simply due to the sheer drama of such stories. Books have been written about these feuds, for example Hal Hellman's Great Feuds series is a good introduction to these historic events.

A classic example is the "Great Race" between Dr. Jonas Salk and Dr. Albert Sabin to develop the first safe and effective polio vaccine. The result of their competition is that since 1955 hundreds of millions of children, including your humble narrator, have been saved from the "Crippler" - a massive benefit to humanity.

Nonetheless, I don't think I can conclude either way. We will need a lot of data in order to tease apart the relative importance of competition and cooperation to science. I'm not even sure if this sort of information is useful for science historians.

Stewing Brainz

An noteworthy article in the Straits Times today. You can click on the link for the full article; only select parts will be highlighted here:

PAP raps WP for ill-timed silence and double-talk

THE People's Action Party (PAP) has criticised the Workers' Party (WP), saying it failed to make its stand clear on important issues at critical points.
WP secretary-general Low Thia Khiang, it added, is often 'quick to criticise, yet offers no serious proposals'.

Taking aim at the WP and the MP for Hougang - in the latest issue of the PAP newsletter Petir - was Dr Ng Eng Hen, who said: 'Singaporeans deserve more from Mr Low and the WP than silence at defining moments, or double-talk when pressed to state their stand.'...


... Another instance was the WP May Day message asking if Singaporeans 'truly benefited' from job creation last year.

PAP MP Seng Han Thong, an NTUC assistant secretary-general, asked at the time if all Hougang Town Council employees were Singaporeans. The WP said they were and added that it did not object to contractors hiring foreigners.

Said Dr Ng: 'This is another cop-out. If the WP truly believes that all jobs should be reserved for Singaporeans, why does it not insist that its town-council contractors hire local workers only?'

The Government, in contrast, has 'a clear stand'. While foreign workers keep the economy competitive, the Government also does its utmost to raise the skills of Singaporeans, said Dr Ng, who is now Education Minister, but previously held the Manpower portfolio...


... Mr Low is out of town. But WP chairman Sylvia Lim responded yesterday.

She said the party's policy positions were clearly laid out in its manifesto at the 2006 General Election.

Since then, the WP took on issues such as the goods and services tax hike, ministerial pay, means testing, constitutional amendments and criminal justice.

On Mr Low's silence in response to PM Lee, she said: 'Benchmarking ministerial pay to corporate pay, but without corresponding corporate consequences, brings to the fore the contentious issue of whether ministers should be paid at top corporate rates. Is the comparison of minister to CEO valid?'

She added that the WP is not against foreign workers.

Rather, given that Singaporeans were told they had to be grateful that foreign workers saved their jobs, the WP questioned 'how far Singaporeans' social standing and prospects have been eroded... Does the PAP not know this is a real ground concern?'


Here at Fresh Brainz, we observe that Miss Sylvia Lim may have slightly under-stated the ground concern, which is not only confined to working-class Singaporeans.

Their anxieties are shared by many other individuals at other levels of society.

This has become a highly sensitive issue and the authorities should manage it with utmost care.

A Cry For Help?

Yesterday, while climbing an overhead bridge to the Buona Vista MRT station, I saw a small wooden board lying on the steps.

It was broken into two pieces, and appeared to have a handwritten message on it.

When I put it back together, this is what it read:

I Wish That I Could Turn Back The Clock

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

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

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

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

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

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

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

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

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

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

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

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

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

Benefits Of Failure, Importance Of Imagination

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





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

My favourite part is:

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

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

Nice.

Pipette tip to BackStage.

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

On The Shoulders Of Giants

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

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

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

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

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


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

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

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

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

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

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

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

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

A tip-less finger!

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

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

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

The brain is responsible for this effect.

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

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

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

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

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

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

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

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

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

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















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

Hey, that sounds extremely familiar!

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

I can't remember the name of that field.


Pipette tip to Mind Hacks.

We Have Always Done It That Way

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

Contingent