Science Reporting By The Straits Times

Just read a science article in the Straits Times entitled "Brain Illness Leaves Woman Fearless." (ST 18 Dec 2010 Page C14)

The research study that is featured in the article (diminished fear experience of a woman with a genetic condition of the amygdala) is quite interesting, but what is even more interesting is how the Straits Times presented the news.

Since the ST article was edited mainly from an original article by Agence France-Presse (with some details from an Associated Press report added in), it is informative to compare the ST and AFP versions to see the differences.

Words that are different or missing in either version are highlighted in RED (additional source marked with asterix).

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ST Version

Brain illness leaves woman fearless

WASHINGTON - United States scientists have discovered a woman with a rare brain disease that makes her afraid of nothing - not a huge snake lurking near her children, not a knife to her throat, and certainly not a horror movie.

The 44-year-old* woman cannot experience fear because of a condition that has destroyed the part of her brain - the amygdala - where researchers believe the feeling of fear is made.

Over the past two decades researchers have been analysing the woman, known as SM, for clues about her condition which they say could help them treat post-traumatic stress disorder, particularly in soldiers returning from war.

A study of her fearlessness was published online on Thursday in the journal Current Biology by University of Iowa researcher Justin Feinstein and colleagues.*

"It is quite remarkable that she is still alive," said Mr Feinstein. "The nature of fear is survival and the amygdala helps us stay alive by avoiding situations, people, or objects that put our life in danger," he said.

Instead of fear, SM, whose rare condition is known as Urbach-Wiethe disease, describes "an overwhelming feeling of curiosity."

The woman's eldest son, who is in his 20s, told researchers he could not ever recall seeing his mother afraid.

He said he remembered one event in particular from his childhood when he was playing with his two brothers and they saw a big snake in the road nearby.

"Well, mum just ran over there and picked it up and brought it out of the street, put it in the grass and let it go on its way," he said.

The woman also told researchers that when she was in her 30s, a man grabbed her and stuck a knife to her throat.

"She looked at the man and confidently replied, 'If you're going to kill me, you're gonna have to go through my God's angels first.' The man suddenly let her go," said the study, adding the woman then described walking calmly home.

Other experiments devised by the researchers - leading her through a haunted house where people dressed as monsters and ghosts sprung from the darkness, and showing her a series of scary video clips - fell flat too.

She considered the haunted house to be "highly exciting and entertaining", like the rush she gets from a roller coaster, Mr Feinstein said.*

Scientists believe she was once able to feel fear because she has described childhood memories of being afraid of the dark, and being once frightened by a dog.

Mr Feinstein said he hopes that SM's experience could help treat people with post-traumatic stress disorder, a problem he has seen in his work treating US soldiers returning from Iraq and Afghanistan.

"Their lives are marred by fear, often times unable to even leave their home due to the ever-present feeling of danger," he said.

"By understanding how the brain processes fear, we may one day be able to create treatments that selectively target the brain areas that allow fear to take over our lives."

*From AP report


AFP Version

Woman who knows no fear could offer brain clues

WASHINGTON - US scientists have discovered a woman with a rare brain disease that makes her afraid of nothing - not a huge snake lurking near her children, not a knife to her throat, and certainly not a horror movie.

The woman cannot experience fear because of a condition that has destroyed the part of her brain - the amygdala - where researchers say they believe the feeling of fear is made.

Over the past two decades researchers have been analysing the woman, known as SM, for clues about her condition which they say could help them treat post-traumatic stress disorder, particularly in soldiers returning from war.

"It is quite remarkable that she is still alive," said lead author Justin Feinstein whose study appears in the journal Current Biology.

"The nature of fear is survival and the amygdala helps us stay alive by avoiding situations, people, or objects that put our life in danger," he said.

"Because SM is missing her amygdala, she is also missing the ability to detect and avoid danger in the world."

Instead of fear, SM, whose rare condition is known as Urbach-Wiethe disease, describes "an overwhelming feeling of curiosity."

To test her reaction, researchers led her into an exotic pet store filled with spiders and snakes, animals she repeatedly said she "hates" and tries to avoid.

"Upon entering the store, SM was spontaneously drawn to the snake terrariums and appeared visually captivated by the large collection of snakes," the study said.

Asked by a store employee if she would like to hold one, SM agreed and then played with one for about three minutes.

"She rubbed its leathery scales, touched its flicking tongue, and closely watched its movements as it slithered through her hands," it said.

"Her verbal behavior revealed a comparable degree of fascination and inquisitiveness: she repeatedly commented, 'This is so cool!'"

When she reached for a tarantula, however, she had to be stopped because there was a high risk she could be bitten.

"When asked why she would want to touch something that she knows is dangerous and that she claims to hate, SM replied that she was overcome with 'curiosity,'" the study said.

The woman's eldest son, who is in his 20s, told researchers he could not ever recall seeing his mother afraid of anything.

He said he remembered one event in particular from his childhood when he was playing with his two brothers and they saw a big snake in the road nearby.

"Well, Mom just ran over there and picked it up and brought it out of the street, put it in the grass and let it go on its way," he said.

"I thought that was kind of weird."

The woman also told researchers that when she was in her 30s, a man grabbed her and stuck a knife to her throat.

"She looked at the man and confidently replied, 'If you're going to kill me, you're gonna have to go through my God's angels first.' The man suddenly let her go," said the study, adding the woman then described walking calmly home.

Other experiments devised by the researchers - leading her through a haunted house where people dressed as monsters and ghosts sprung from the darkness, and showing her a series of scary video clips - fell flat too.

"She reacted to the monsters by smiling, laughing, or trying to talk to them," the study said.

"She found the fear films to be exciting and entertaining, and in one case, she inquired about the name of the movie so she could rent it from the video store later that day."

Scientists believe she was once able to feel fear because she has described a childhood memory of being afraid of a dog.

They also note that "SM has never been convicted of any crime, but rather has been the victim of numerous crimes."

Feinstein said he hopes that SM's experience could help treat people with post-traumatic stress disorder, a problem he has seen in his work treating US soldiers returning from Iraq and Afghanistan.

"Their lives are marred by fear, often times unable to even leave their home due to the ever-present feeling of danger," he said.

"By understanding how the brain processes fear, we may one day be able to create treatments that selectively target the brain areas that allow fear to take over our lives."

Feinstein said science should look for PTSD treatments that "focus on ways to safely and non-invasively dampen amygdala activity," mainly through medication and psychotherapy.

~~~~~~~~~~

A significant portion of the original AFP article is omitted from the ST version.

Interestingly, the missing parts are mostly related to the downside of having practically no fear, such as the inability to detect and avoid danger, fascination with potentially dangerous animals, becoming a victim of crimes etc.

A quick survey of other new reports indicates that this danger of lacking fear is actually an important message from the researchers - here are some excerpts:

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1. Associated Press

a) Her case shows that the amygdala plays a key role in making people feel afraid in threatening situations, researchers say.

Her life history also shows that living without fear can be dangerous, they said.

b) She apparently hasn't felt fear as an adult, not even 15 years ago in an incident described by the researchers. A man jumped up from a park bench, pressed a knife to her throat and hissed, "I'm going to cut you."

SM, who heard a church choir practicing in the distance, looked coolly at him and replied, "If you're going to kill me, you're going to have to go through my God's angels first."

The man suddenly let her go. She didn't run home. She walked.

"Her lack of fear may have freaked the guy out," Feinstein said.

But it also got her into that situation in the first place, he noted. SM had willingly approached the man when he asked her to, even though it was late at night and she was alone, and even though she thought he looked "drugged out."

SM has also walked into other dangerous situations because of her lack of fear, and all in all, it's remarkable she's still alive, Feinstein said.


2. ABC News

a) S.M. also had exposure to fearful situations in her past. She was held up at gunpoint and at knifepoint and was almost killed during a domestic incident. S.M. told researchers she did not feel fear during these life-threatening situations. She was also aware that her inability to react to fearful stimuli was not normal.

b) S.M.'s case is also important to understand because the ability to experience fear and respond to it is essential to survival. The researchers believe that because she could not detect threats to her safety and avoid them, she wound up in numerous life-threatening situations.

"Indeed, it appears that without the amygdala, the evolutionary value of fear is lost," the authors wrote.


3. Time.com (Healthland)

a) The authors note that SM's response to what would normally be considered fear-inducing situations was not characterized simply by a lack of responsiveness, but rather a heightened arousal and interest. In other words, she practically courted danger.

b) The researchers stress that SM's condition is more a curse than a blessing: "[SM's] behavior, time and time again, leads her back to the very situations she should be avoiding, highlighting the indispensable role that the amygdala plays in promoting survival by compelling the organism away from danger. Indeed, it appears that without the amygdala, the evolutionary value of fear is lost."


4. Discovery News

a) That wasn't the only occasion that SM, who was living in the projects in a seedy part of town, got herself into a precarious situation. There was the time, for example, that a man approached her from behind, put a gun to her head, yelled "Boom!" and then ran away. She figured her attacker was a drug dealer whom she had repeatedly turned in to the police, but she didn't consider calling the cops after the incident.

"She described the situation as strange," Feinstein said. "She's not reacting in normal ways that anyone who had fear would."

b) "We don't suggest by any means to remove this area of the brain," Feinstein said. "We don't want a million SM's walking around getting in trouble. This one case highlights why we do need an amygdala."

Instead, it's possible that drugs or behavioral methods could quiet the amygdala just enough to free people whose lives have been taken over by fear.


5. Scienceblogs.com (Neurophilosophy)

a) SM has been studied extensively during the past two decades. Early investigations showed that her non-verbal visual memory was signficantly impaired but that otherwise she had an IQ in the low-average range. She also displayed inappropriate social behaviours, quickly becoming friendly with the experimenters and making sexual remarks, due to disturbed executive control. Subsequently, it was found that she was unable to recognize emotions in facial expressions, and a study published earlier this year showed that the brain damage had eliminated her monetary loss aversion - that is, she makes risky financial decisions that most of us would avoid because of a fear of losing money.

b) But based on interviews with her and her three children, the authors suggest that she probably has not experienced fear at all throughout the whole duration of her adult life, despite having encountered an unusually high number of traumatic and life-threatening events. Aged 30, she had a knife held to her throat by a drug addict while she walked through a park at night, but did not panic and walked away calmly when he let her go. She has also been held at gun point, was nearly killed in an act of domestic violence, and has been the victim of numerous crimes in the poverty-stricken area in which she lives.

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From these excerpts, it can be seen that all the above news articles - except for the Straits Times version - emphasize the researchers' point about the dangers of lacking fear.


Would you like to know more?

- The Human Amygdala and the Induction and Experience of Fear (Feinstein et al. 2010) Current Biology

A Grey Lizard That Isn't Really Grey

Last month, during the Chinese New Year period, I was passing through a jogging track beside a canal in Ghim Moh when I spotted this little critter:















GREY LIZARD!

It had a surprisingly deep grey colour that matched the surrounding asphalt very well. If not for the fact that it was dashing across the track right in front of me, I would have missed it.

I think that its grey skin is a good camouflage to protect the lizard against predators, such as birds.

I don't know much about lizards, but I find its even grey tone surprising since I've only seen garden lizards in brown and green.

My first thought when I saw it was - maybe there is a selection pressure for "jogging track lizards" to be grey?















Here's the fellow next to a ten cent coin.

The lizard was about 3 cm long. It could be a juvenile, so the grey colouration could be a transitory feature.

Most scientists who study the evolution of animal features tend to focus on the adult form. That doesn't mean that the features of young animals are less important.

We must remember that the environment starts to act against an animal, even before it was born!

If an animal cannot survive its youth, it cannot become an adult.















When I took a close-up photo of the lizard, I realized that it wasn't really grey!

The scales were in a mottled pattern of light and dark brown, and coupled with the fact that the lizard appeared to be moulting, the resultant colour from a distance was a dull, dark grey.

It made me ponder about the concept that quantitatively different features at the component level can result in qualitatively different features at the system level, ie. emergence.

After all, if you try to find a novel "grey gene" on this grey lizard, you might end up finding nothing! It might have been the combination of expression level changes to existing brown colour genes and opacity of the scales that contributed to its overall grey appearance.

Well, that's too much speculation for one day.

So I left the lizard, which had remained frozen in that position for minutes on the asphalt and didn't leave even after I had walked several metres away.

Survival instinct or excessive fear?

Seconds later, a bicycle zipped by that same spot.

I didn't look back.


Would you like to know more?
- Tertiary color (Wikipedia)

The Problem-solving Intelligence Of Bird Brainz

Picture this - you are a hungry bird and you are looking at a fat, juicy worm.

Unfortunately, the worm is floating on a bit of water in a very tall glass, and your beak is not long enough to reach it.

What do you do?



Sharp.

That practically replicates the Aesop's Fable "The Crow and the Pitcher"!

Is that a particularly smart bird, you ask?

Actually, four out of four rooks in the experiment were able to figure out this solution to the problem.

An elegant demonstration that problem-solving intelligence at least predates the evolution of mammals.

Pipette tip to Bayblab.


Would you like to know more?
- Rooks Use Stones to Raise the Water Level to Reach a Floating Worm (Current Biology)

Creationism And False Dichotomies

Lim Say Liang at The Online Citizen has written an interesting article entitled "God sneaks into our classrooms" about how creationism has turned up in Singaporean schools.

I understand that creationism is formally not acceptable by the MOE, so I have nothing to add to that discussion from an education policy point of view.

From the scientific perspective, as Dr. John van Wyhe from Cambridge has emphasized in his recent talk, there has been no debate between evolution and creation since the 1870s.

Evolution - more specifically the part about common descent - has been accepted by the scientific community for over a hundred years.

However, debate about the details of evolution, such as its primary mechanism (eg. natural selection vs neutral drift) continues on today.

This sort of dispute is usually only interesting among specialists (may sound very boring to the general public) but will be gradually resolved in time with theory development and more experimental evidence.

On the other hand, the "Evolution vs Creation" culture war (and predominantly US culture at that) is a very tiresome and possibly neverending squabble that will persist as long as people, politics and money exist.

I won't go into the details of this - interested readers can just click the "evolution" tag to see my numerous articles (and even more numerous comments) regarding this topic.

Instead I would like to focus on a pair of comments posted in response to the TOC article -


1. New Renaissance on August 3rd, 2009 2.33 pm:

"In fact, what critical thinking can there be if only one side is presented?"

2. Jer Bear on August 3rd, 2009 3.09 pm @ New Renaissance:

"The other side of science is not fiction. The other side of science is science itself. One cannot disprove logic with fairy tales – therefore if you truly believe in teaching our children critical thinking, show them the thousands of articles written to refute certain scientific and mathematical explanations. Creationism or ‘intelligent design’ doesn’t count."


I think Jer Bear has addressed the New Renaissance's criticism quite well, but I would like to add my views on this matter.

I have observed that creationists like to think of science as if it was some kind of legal process and like to think of scientists as if they were lawyers.

In fact, creationist lawyers tend to think that their legal training makes up for their lack of scientific training.

Why is this so?

Simple.

Dichotomies, even false dichotomies, have a lot of SOCIAL POWER.

Remember ex-US president George W. Bush's infamous line: "Either you are with us, or you are with the terrorists."?

A legal system is an adversarial system. Either a suspect is innocent or guilty. There is no middle ground and thus no need to consider alternative explanations.

By proving your opponent wrong, a lawyer can confidently "prove" that she is right.

When deliberately forced upon science, this legalistic perspective crushes the whole scientific process into an oversimplified single dimension with two absolute outcomes: right or wrong.

That is why creationists spend practically all of their time attacking science rather than do actual research to support their views.

To their credit, they do understand the human psyche very well; the general public is easily impressed by outward appearance of authority, conviction and eloquence. As long as they can "prove" that the scientists are unsure, or hesitant, or not very good at public speaking, or too easily annoyed, creationists can then claim success.

This can be done without actually addressing the scientific content of the argument; indeed, it can be done without adequate understanding of the subject matter at all!

That is because creationists are not as interested in knowing what is factually correct as they are obsessed about being "proven" right. If they are "proved" to be right they can consolidate the social cohesion among fellow believers and also feel that they have the justification to impose their worldview on everyone else.

To directly address New Renaissance's comment that there can't be any critical thinking if only one side is presented, I would say:

"Are there only two sides in every debate? What critical thinking can there be if only two sides are presented?"

If the subject matter is creation stories, why not present a multicultural primer about creation stories throughout the world? If the focus is on anti-evolutionary views, why not include a section on animal spiritualism and Hare Krishna's "devolution" idea?

Creationists will never advocate multifactorial thinking, because it weakens their case that they can be "proved" right as long as their opponent is "proved" wrong. If there are ideas that don't support their case, they will cleverly package all of them together into a single opponent, even if those ideas don't have much in common with each other.

Eventually they will try to force an adversarial approach in order to maximize their social power.

Only the debates between "us" and "them" matters; disagreements between them "evolutionists" or disagreements between them "pagans" don't matter.

They are all wrong anyway... because my belief "proves" it.

Rise Of Creationism In Asia

Brandon at The Biology Refugia wonders why the creationist/ID movement has suddenly gained prominence outside of the USA in the past ten years or so.

I see the rise of the movement more as an incremental phenomenon, though likely spurred on in recent times by eight years of the Bush administration.

Monuments of ignorance such as the Creation Museum and the Discovery Institute have undoubtedly ignited the enthusiasm of others who are interested in replicating these impressive results in their own country.

Brandon also asked:

"So, future intellectual historians of our times: why is this happening now? And why simultaneously in societies so different from each other and from the US, where all this started?"

That's a great question - an interesting consequence of globalization is that with the increased exposure to travel and mass media, two people in one "society" of a country can have practically nothing in common, whereas two people living in different continents may share practically the same motivations and goals.

This has and will continue to create tensions between people living in the same "society" who share the same nationality, ethnicity, language and cultural history but yet have completely different or even conflicting worldviews.

Yau-man Chan at the Skepticblog puts it this way:

"The problem I have with Chinese fundamentalist Christians is how could they discard their own history? For better or for worse, we come from an ancient culture and definitely have the baggage to show for it. We have written history as old as any Middle Eastern civilizations. We have our own legends and sagas to tell the stories of our glorious ancient past. So how can a Chinese, knowing his own culture and historical past become a Young Earth Creationist? How can a person have two histories? What kind of mental gymnastic must my YEC classmates perform to adopt the Genesis stories as real and to discard the narratives of our forebearers was mere legends?"

Considering that respect for our ancestors and cultural history is an integral part of many East Asia societies, it is curious to observe that so many people are abandoning their own identity and embracing a foreign culture wholesale.

Perhaps their own local culture is not atas (high class) enough for them.

In any case, it is interesting to discuss how these people insist on "traditional values" that are not really traditions in their own culture but are actually imported "traditions" from a Western country, eg. USA.

What do you think?

No Really, I CAN See Through You

Sometimes I wonder if deep sea fish aren't really Aliens from another planet...




Well, at least Macropinna microstoma doesn't have zombie eyes and Giger-esque teeth like the deep sea fish in my profile.

In fact it's rather cute, in a revulsive-ectoplasmic-anime-character-from-hell sorta way.


Would you like to know more?
- Weird-eyed fish (Pharyngula)

FAMILIAR Part 4: Aligned Resources

One important reason why the Star Wars series of films has such a wide appeal is due to its story structure. George Lucas was inspired by Joseph Campbell's book, The Hero with a Thousand Faces, and deliberately applied Campbell's ideas into his storyline.

Campbell was studying comparative mythology and wanted to find out if there are common elements between major myths around the world that have lasted for thousands of years. He elucidated a fundamental structure which he called the "monomyth" or "the hero's journey" and summarized it like this:

A hero ventures forth from the world of common day into a region of supernatural wonder: fabulous forces are there encountered and a decisive victory is won: the hero comes back from this mysterious adventure with the power to bestow boons on his fellow man.

The monomyth is divided into three sections - "Departure", "Initiation" and "Return". Each of these sections has a set of characteristic stages, for example "Supernatural Aid" in Departure where the hero encounters an old wizard (Obi-Wan!) who provides him with special tools (Lightsabre!) and advice (Use the Force!) for the adventure ahead.

Only a few world myths contain all these stages, some of them only have a few stages and others have them in a different order. Campbell's monomyth is thus criticized for focusing on the similarities and glossing over the differences between the myths, and scholars have also questioned its usefulness and general validity.

Nonetheless the monomyth has been an influential tool for plot development; aside from Star Wars, popular movies like The Lion King and the Matrix series (possibly the Harry Potter series as well) have story structures that are modelled on the monomyth.

I won't go into further details of the monomyth here, but suffice to say that by using a comparative strategy, Campbell was able to create a common resource out of the dozens of diverse mythologies in the world. He recognized that it is impossible to do this based on any single myth.

Indeed, I would argue that in general single cases only represent data and not knowledge. Outside the context of mythology, even single cases that are firmly rooted in physical evidence cannot really enlighten us about the nature of our Universe; we can only learn about them, not from them.

In other words, they have descriptive but not prescriptive value.

**********

The power of comparative analysis was driven home in my mind very early in my graduate student career by my advisor.

During a genomics lecture he illustrated this by showing a single sequence from one species of animal. For example, here's part of the amino acid sequence of a human gene:

MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRPMNAFMVWSRGQRRKMAQEN...

Well, it's a string of letters. You can't learn much just by staring at it.

But when you do an alignment with homologous genes from many other species...






... important features immediately jump out at you.

The yellow blocks represent regions that are completely identical over hundreds of millions of years of evolution - it's a good bet that those regions are functionally crucial. Blue and green blocks are identical only among some species, while white areas exhibit high variability.

Therefore, you can see regions of similarities as well as regions of differences. Regions that are common to mammals, or just to rodents, or unique to one species which may reflect functions that are only relevant to those group of animals.

This is knowledge.

Whether it is science or history, information derived from a single case is only descriptive of the case itself - in order to understand fundamental principles, produce testable predictions or to "give advice" to other people, you must have data from more than one case. With an increasing number of aligned cases comes a more accurate and more refined knowledge of the subject matter.

Hence the "analogy" aspect of FAMILIAR - knowledge obtained by comparing the features of complex systems and aligning them into a structured resource, not only at the same organizational level, but also across organizational levels.

I am aware that argument from analogy is a logical fallacy, but that does not preclude the use of an "analogy machine" like FAMILIAR to start the investigation by generating hypotheses and enabling cross-discipline visualization.

Having a systematic way to align single cases into a common resource allows people to see both the similarities and differences between the cases. Where the cases are too different in key areas to be effectively compared, proposed models can be rejected as uninformative. Where cases have striking similarities over numerous key characteristics, there is compelling support for a fundamental structure among them.

However, human knowledge is wildly varible in format. How is it possible to align diverse forms of knowledge into one common resource?

Stay tuned for the next post on the FAMILIAR Core.

FAMILIAR Part 3: General System Theory

Ludwig von Bertalanffy was an Austrian-born biologist who was a major figure in the development of the systems theory.

Around the mid-20th century he was concerned about the overemphasis on the reductionistic approach and the resulting fragmentation of science. In 1968 he published his book General System Theory where he wrote:

A consequence of the existence of general system properties is the appearance of structural similarities or isomorphisms in different fields. There are correspondences in the principles that govern the behaviour of entities that are, intrinsically, widely different. To take a simple example, an exponential law of growth applies to certain bacterial cells, to populations of bacteria, of animals or humans, and to the progress of scientific research measured by the number of publications in genetics or science in general.

System isomorphisms also appear in problems which are recalcitrant to quantitative analysis but are nevertheless of great intrinsic interest. There are, for example, isomorphies between biological systems and 'epiorganisms' like animal communities and human societies.

It seems therefore that a general system theory of systems would be a useful tool providing, on the one hand, models that can be used in, and transferred to, different fields, and safeguarding, on the other hand, from vague analogies which often have marred the progress in these fields.

Bertalanffy, together with some of his contemporaries, noted that regulation via feedback loops allow a system to maintain stability (today this field of study is called cybernetics).

He was also interested in the apparent contradiction between the 2nd law of thermodynamics and the increase in organizational complexity of living systems during embryo development and evolution. He proposed an idea that resolves this:

According to the second principle of thermodynamics, the general trend of events in physical nature is towards states of maximum disorder and levelling down of differences, with the so-called heat death of the universe as the final outlook, when all energy is degraded into evenly distributed heat of low temperature, and the world process comes to a stop.

In contrast, the living world shows, in embryonic development and in evolution, a transition towards higher order, heterogeneity, and organization.

But on the basis of the theory of open systems, the apparent contradiction between entropy and evolution disappears. In all irreversible processes, entropy must increase. Therefore, the change of entropy in closed systems is always positive; order is continually destroyed.

In open systems, however, we have not only production of entropy due to irreversible processes, but also import of entropy which may well be negative. This is the case in the living organism which imports complex molecules high in free energy. Thus, living systems, maintaining themselves in a steady state, can avoid the increase of entropy, and may even develop towards states of increased order and organization.

Bertalanffy's concept of an open system is usually illustrated like this:















Input refers to the stimuli and imported materials from the external environment, throughput refers to the processes within the system, and output refers to the resulting response or exported materials.

To emphasize the importance of feedback control, this version is also used:














Bertalanffy's open system model inspired biologist James Grier Miller to examine the applicability of systems theory to living systems.

Miller published Living Systems Theory in 1978, expounding his general theory about the existence of all living systems, their structure, interaction, behavior and development. He proposed that living systems must contain 20 critical subsystems which he later arranged into 8 nested hierarchical levels:















Miller noted that:

All nature is a continuum. The endless complexity of life is organized into patterns which repeat themselves—theme and variations—at each level of system. These similarities and differences are proper concerns for science. From the ceaseless streaming of protoplasm to the many-vectored activities of supranational systems, there are continuous flows through living systems as they maintain their highly organized steady states.

His observation of recursive patterns is likely to be inspired by the work of Benoît Mandebrot, the mathematician who founded the field of fractal geometry. Mandebrot observed that many objects in nature exhibited self-similarity and scale invariance - parts that are made up of smaller scale versions of the overall shape.



















Interestingly, neither Bertalanffy nor Miller made any big impact on the field of biology itself, which in the wake of monumental discoveries of DNA and the central dogma, has remained firmly rooted in the reductionist paradigm.

General System Theory has become influential mainly in information science and cybernetics, whereas Living Systems Theory is more commonly read in sociology.

That is why as a neuroscience undergrad I had never heard of these guys and was completely unaware of systems theory, even though I regularly lamented with one of my fellow students about the lack of a systems interpretation of neuronal behaviour.

I first read Bertalanffy in 2005 when I picked up his General System Theory from the NUS library during the height of the popularity of the buzzword "Systems Biology". I wanted to know all this "systems" talk really meant, apart from expensive, shiny new high-throughput liquid handling robots.

I found his book to be quite repetitive but I was impressed by his open systems model, which I now call the "Bertalanffy Box". Excitedly, I wrote an article about it which was published in a student's magazine (GSS Journal 2005).

Here is an exerpt:

Actually, Systems Biology is not strictly a new idea. Some aspects of this perspective can be traced as far back as Plato! The modern synthesis of its fundamental concepts, however, first appeared in the General System Theory (GST) proposed by biologist Ludwig von Bertalanffy in the late 1940s. At that time, Bertalanffy was disturbed by what he saw as the overspecialization and fragmentation of science. He felt that the standard reductionistic approach to science was driving scientists to obsess over tiny details that may not advance the understanding of the big picture. His solution was to find some common patterns of organization in nature which could help unify the sciences and even the humanities together.

In a nutshell, the GST is a holistic theory that describes a complex system by examining the interactions between its components, rather than by analyzing the detailed structure of each component. Gesalt psychologists say that “the whole is greater than the sum of its parts,” an illustration which is also valid for the GST. In the context of biology, Bertalanffy described living organisms as “open systems” that interacts comprehensively with their environment. Next, he recognized that complex systems have emergent properties that cannot be predicted by knowing the properties of its components. In addition, he observed that such a system can also exert control over its components, such as in homeostasis, by using feedback loops.

Although I liked the simplicity of the Bertalanffy box, I found it to be incomplete and aesthetically displeasing. It is only focused on one particular system and has no scaleable aspects, thus it cannot take into account the inputs that might have arrived from another organization level, and ignores the outputs that will affect another organization level.

While recuperating from an illness in a hospital, I decided to improve the Bertalanffy box by integrating Bertalanffy's idea with Mandebrot's (I hadn't read Miller yet), and this is the result:















The "extended" Bertalanffy box (which I called a "leaky" open system at that time) features a system that is affected by both internal and external inputs and contributes outputs to both internal and external states. Thus, it is embedded in an organization level with constant interactions with lower, adjacent and higher levels.

Now I had a repeatable unit that is scaleable and conceptually self-similar.

To illustrate the self-similar aspect in a more visually striking manner, I designed this diagram about a year ago:















Here you can see a complex system opened to reveal the interactions in its intrinsic environment. It is made up of complex systems which are in turn made of smaller complex systems. With this simple repeating unit, you can model a system of any amount of complexity.

I hope I have clearly explained the "Fractal" aspect of FAMILIAR.

But what about the "Analog" part?

Stay tuned for my next post on heroes' journeys and multispecies alignments.

FAMILIAR Part 2: Why No Runaway Complexity?

Long time Fresh Brainz readers probably know that my undergrad training was not in molecular biology, but in neuroscience.

My interest in systems science started about 10 years ago when I learnt a bizarre fact about neurons - that the transmission of neural impulses was a probabilistic process.

The firing of a neuronal action potential is not perfectly reliable because it depends on a complex interplay of input signals such as EPSPs, IPSPs and internal states such as the refractory period.

Due to the inherent unpredictability of any single neuron, vertebrates have to rely on a large number of neurons in each nerve in order to convey a reliable signal to other parts of the body.

This struck me as something that is particularly odd.

If you can't even trust one neuron to do its job, how can you trust a thousand of them?!??

Why won't they simply misfire all over the place and garble the signal?

The nervous system has often been compared with human technology such as computers, but you'd be barking mad to try design a computer using millions of components that are not 100% reliable.

These questions perplexed me during my undergrad years and also in my first job as a research assistant in neuroscience. What was even more puzzling then was the realization that other researchers around me simply took this fact for granted - nobody would explain to me why a bunch of unreliable parts could suddenly make a reliable system.

As I started grad school in 2004, I noticed that a similar situation occurs in cell biology. In an unfinished article entitled "Brief thoughts on the Inception of Systems" I wrote:

A cell is an amazing mixed bag of biochemical processes, some of them quite straightforward, others so convoluted that Occam’s razor would not find its mark there.

Unlike the oft used analogy of a factory, each cell is made up of components that do not fit together clearly like a clock. For example, many proteins have multiple roles across several different pathways. From cell to cell, proteins can have different functions depending on where and when it is expressed.

The compounded variability from the probabilistic performance of each intracellular player should become so large so as to make an integrated system impossible.

What I am saying is, if one wanted to make a reliable machine to fulfill a very specific function, one would not deliberately use components with variable and probabilistic characteristics. But yet cells do exists, and are quite stable and reliable. How can this be?

How indeed?

Let me illustrate this problem with a graph.















When the number of components in a system is small, the total number of interactions is limited and predictability of component behaviour is high.

This is why we can play games like pool and snooker - we can tell where the target balls will end up.

As the number of components increase, the total number of interactions increase exponentially to such an extent that it quickly becomes impossible to know exactly what will happen.

Imagine a pool table with thousands of balls.

In addition, the probabilistic behaviour of each component makes this problem far, far worse.

Imagine a pool table with thousands of unbalanced balls!

By this additive concept, it should be impossible for any limited sentient being to comprehend much of the Universe, since it consists of trillions upon trillions of probabilistic subatomic particles in constant interaction.

But here lies the trick...















In some cases, the increasing number of components start to exhibit emergent properties, forming a complex system. The whole system itself becomes reliable enough to be a "component" (or module) of another larger system.

Each successive complex system then occupies a higher organization level in a hierarchical structure, so that the total number of "component" interactions at the higher organization level never gets out of hand.

This why we can predict the trajectory of a cannonball with such accuracy, even though we can never predict the exact locations of all the component electrons in a cannonball.

There is no runaway complexity because complexity appears "fold in" on itself with each successive organization level.

But how exactly does a complex system make itself reliable and predictable?

Stay tuned for my next article about Ludwig von Bertalanffy and his General System Theory.

FAMILIAR: Unity of Knowledge

It is with great reluctance that I reveal my new model of organizing and creating new knowledge, called FAMILIAR (Fractal-Analog Method of Integrating Limitless Information into Aligned Resources), partly because I had planned to refine this idea further so that I can publish it properly in a book, and partly because I'm not best friends with humanity right now and I don't want my ideas to fall into the hands of the people I hate.

As it currently stands, the model has some holes and is fairly useless, but when decked with sufficient relevant data it has some potentially powerful implications.

This is an exclusive privilege for Fresh Brainz readers only - please do not pass this knowledge to scumbag bankers, dickhead politicians and fuckfaced lawyers because they can turn this idea into a weapon for controlling everyone.

Many thanks.

**********

"The most incomprehensible thing about the world is that it is at all comprehensible." - Albert Einstein

Indeed, considering its complexity and vastness, the most mysterious thing about the Universe is the fact we can even begin to understand it.

Strangely enough, the reality is that the vast majority of living systems are routinely capable of coping with the staggering complexity of the Universe. People and microbes alike experience perfectly happy lives without needing to know the existence of quarks or quasars.

The key to this is the ability to prioritize and react only to a few immediately relevant aspects of the total complexity - to differentiate between knowledge and data.

Scientifically, "knowledge" comprises a collection of data (or fact) and an explanatory structure (or theory) that organizes the data into a meaningful whole. While data constitutes an important aspect of knowledge, by itself it is not knowledge. In fact, data that cannot yet be aligned into any coherent explanatory structure will usually be regarded as noise.

It doesn't take a genius to perceive the difference between knowledge and noise; the tiniest single-celled organism instinctively ignores most of the stimuli it receives from its environment and responds to only some of them that pose an immediate threat or benefit.

Likewise, scientific knowledge doesn't directly mimick the full complexity of a given system, but brutally simplifies it into some basic principles that are comprehensible and useful to the human mind, thus allowing testable predictions and technologies to be produced.

This simplification process is often accused by opponents of rational inquiry to be fatally flawed because it is unavoidably tentative and incomplete.

How can anyone claim to understand the whole Universe if one has only examined an infinitesimal fraction of it?

Here at Fresh Brainz, we think that such a feat is possible once you appreciate the crucial distinction between knowledge and data, and understand the core structure of systems that reiterate themselves over and over again, from the subatomic world, through the intricacies of cells, organisms and societies to the interactions of galactic clusters.

I should emphasize again that as limited beings we can never hope to collect every last bit of data about the Universe, but we can achieve an increasingly complete knowledge about the Universe.

FAMILIAR is a simple, scaleable model that seeks to organize and unite all aspects of human knowledge so that we can learn about the core structure of systems and in doing so, gradually approach a complete understanding of our Universe.

Stay tuned for the next post about runaway complexity.


Would you like to know more?
- Prologue to FAMILIAR: Redundancy Redundancy

History Of Money

A couple of weeks ago, I went to the Singapore Mint to visit its coin gallery.

I was expecting to see a few glass cabinets with lots of shiny coins inside, but it turns out that the gallery contains much more than that. In fact, it is an exhibition on the history and evolution of money.

To many people living in Singapore today, foreigners and locals alike, Singapore often seems to be a bizarre place, more akin to a trading post than a nation state. The idiosyncrasies of a country can be better understood if you are familiar with its history, and no history of Singapore can be complete without the history of its money, the lifeblood that has nourished and shaped Singapore into its current form.

Enough of the talk; let's go check out 'em coppers and silvers!

*Cha-ching!*















The Singapore Mint is located at Teban Gardens Crescent, in an industrial area together with factories of prominent brands such as Carrier and Leica.

If you are going there by bus, note that it is at least a 5-10 minute walking distance away from the nearest bus stop. Click here for a map, bus guide and driving directions.



















Here's the entrance of the coin gallery, shaped like a coin die with the words "Striking A Legacy" adorning it.

Nice.

The gallery is open from Mondays to Fridays, 8.30am to 4.30pm, and closed on Saturdays, Sundays and public holidays. I've checked with the counter staff that photography is permitted inside the gallery.

Admission is free.















The first thing that greeted me at the entrance is this huge round stone, used by the natives of Yap Island in the Pacific as a form of money and a symbol of wealth.

As you can see from the old photo on display, these islanders have really big rocks.

Own it, flaunt it baby!















To start at the beginning, early human societies did not need money.

Instead, they relied on bartering for trade.



















Here is a photo of a barter contract (carved in stone) used in ancient Egypt over 3000 years ago to exchange a bull for variety of goods including grain, oil, honey, cloth and wood.

Over time, as the variety of farm produce and manufactured goods increased in number, it became more and more unwieldy to use the barter system.

The problem is that each pair of goods will need a standard exchange rate, and when you have thousands of goods, the staggering number of possible permutations will turn trade into an inconsistent and inefficient mess, kinda like Forex gone mad.

I didn't notice it when I took this picture, but while I was editing the shot at home I saw the modern numerals "5649" on the upper left part of the stone contract. I presume that it is the catalogue number for this historical artifact.

Thinking of buying 5649 for 4D?

Who knows, you might win a bag of flour, three ducks, a couple of chickens, half a bucket of milk and a string of pearls!















And so money was invented.

In many parts of the world, money was initially made up of stuff that was convenient to trade with and good for the munchies too - the "commodity currencies" of its day.

Take rice, for example.

Nom nom nom nom...















Tobacco.

Puff puff puff *tarik* puff...















Almonds.

Nom nom nom nom...















Cowries.

Nom nom *KINK!*

Ow ow...

With the advent of cowrie money in ancient China, the concept of money slowly drifted away from commodities and towards representative currency.

Amazingly, cowries were still used as money in some parts of the world until the 1940s.















Money gradually evolved into the forms recognizable to us today.

In China, spade and knife-shaped copper tokens were invented around 2600 years ago. The familiar round coin with a central square hole appeared some 400 years later.















In Europe, coins were made from a natural alloy of silver and gold, called electrum. They were made by striking the lump of metal with a die. The first electrum coins were invented by the Lydians of ancient Greece, also around 2600 years ago.















Later on, coins were made from less precious metals. Ancient coins tend to look fat and irregular in shape compared to modern coins - those were the days before mechanization and mass production.















Let's move on to the story of money in Singapore!



















But first, here's a bunch of trivia for all you touristy-types.

I'm a sucker for trivia.

With so many coins and notes in circulation, there must be literally thousands of dollars that are lost somewhere - dropped inside a drain, tucked in the corner of a bus or stashed in an abandoned warehouse.

Sometimes I fantasize about inventing a giant machine that can find all this lost money, collect it and deliver it to a certain needy student.



















Oh and did you know that we used to have an aluminium 5-cent coin? I saw an uncle selling these coins in a Chinatown kiosk before, but I wasn't sure if it was real.

Aluminium coins feel so light and plasticky - a strange choice of metal for circulation coins. Yet it is quite common to find small denomination coins minted in aluminium - for example in China and Japan.















Now for some historical facts and artifacts!

Everybody knows that modern Singapore was founded in 1819, but betcha didn't know that our first money did not come from the British.

It was the Spanish Dollar, declared as the first legal currency of the settlement in 1823.

In those early days, the Spanish dollar was joined by the Mexican dollar (shown above), Dutch guilders, Indian rupees, Javanese rupees and Penang pice in a mixed bag of circulation coins.















Here are some Indian coins that were used in Singapore. A first attempt was made in 1824 to mint a set of standardized local coins but it was not successful.















After the Straits Settlements became a Crown Colony, the government introduced a new set of coins ranging from 1/4 cent to one dollar in 1871.

It's so weird to see coins minted in fractional cents. Today, the one-cent denomination is practically defunct in Singapore, but obviously it was worth much more at that time.

You can tell that just by the size of the coins; these 1/2 cent coins are as large as modern 20 cent coins...















...and this one cent coin is larger than a modern 50 cent coin!

In fact I don't think I've ever seen such a big copper coin before.

Actually I've always wondered why the British government had to wait until 1968 to decimalize their own coin system when they have already done so in the colonies for around a hundred years.

Hmm...















By the 1930s, circulation coins have shrunken in size and the one cent coin has taken on the familiar square shape.

I call them "Ah Kong Ah Mah coins" because my grandparents left me a small bag of these.















Here's a classic square cent on display, still sporting a bit of copper sheen. In contrast all of my coins have lost their shine and are dark brown in colour.















Fractional cents becoming an endangered species...















Notice the black discolouration on this 5 cent coin?

Yes my friends, it is made of silver! I suppose 5 cents at that time was deemed valuable enough to be minted from precious metals.

It's too bad that silver coins were demonetized in 1949 - today most coins are made from cupro-nickel instead.















This is a collector's set of the first series of Singapore's national coins. You can see the big "Lion" one dollar coin featured prominently at the centre.

According to an old uncle that I spoke with before, the Lion coins apparently didn't see much circulation. People were hoarding them as collectables and spending paper dollar bills instead. Nowadays, large numbers of these coins have emerged from hiding and retailers are selling them for $3 a piece, which is a fucking rip-off.

I should also mention that the problem with collector sets like these is that the coin compartments are not air-tight and so the coins will slowly oxidize over time if you don't keep them in a dry box. The one cent coin is especially prone to discolouration and dark spots.

Professional numismatists recommend that you should leave an aging coin alone and not try to clean it, since a botched cleaning attempt will destroy the value of a collector's coin.















Aside from coins, the gallery also features a small collection of paper money.

Here's an example of a "Post Bill" which first appeared in 1859 as an early form of banknotes.

You can see from the three additional languages in the margins of this bill (clockwise from left: Jawi script, Tamil script, Traditional Chinese characters) that Singapore has been multicultural from the get go.















A later series of banknotes issued by the Board of Commissioners Currency Malaya, featuring the portrait of King George VI.















A dark period in Singapore history - "Banana Notes" issued by the Imperial Japanese Army during the Second World War.

Notice that there are no serial numbers on any of these notes. The Japanese Army printed so many of them that they became worthless by the end of the war.















The old Orchid-series and Bird-series of national dollar bills.

Sometimes I miss the one dollar bill - it reminds me of my childhood when I opened my Ang Pows during the New Year to find a neatly folded stack of crispy, fresh-smelling Bird-series singles inside.

Delightful!















And finally, $10000 and $1000 specimen notes from the current Portrait-series, encased in glass.

What is notable about these bills - apart from the fact that they are clearly too large to fit properly in a wallet - is that they have gold-coloured holograms instead of the silver-coloured ones found on smaller notes.















Next, there is a small section in the gallery dedicated to minting technology.

This is a nice painting that illustrates two ancient methods of making coins - the Chinese method of casting coins by pouring molten metal into tree-shaped moulds, and the European method of striking coins from metallic blanks using dies and anvils.



















The modern method of minting coins is shown here.

An approved design is engraved on two plaster moulds and converted through rubber and epoxy moulds before it is scaled down by a machine to create a master die. Working dies are then made from it.















Ah, the business end of the minting process!



















The rest of the gallery showcases the various commemorative coins and special collector's coins made by the Mint. I won't go into the details of these displays, but I'll highlight two areas that are interesting to me.















One of them is this collection of electronic CashCards - the future of money!

Actually I've always thought that CashCards occupy an odd position between credit/debit cards and cash, sort of like how APS was stuck between digital photography and 35mm film.

While I'm sure that there will always be some niche use for CashCards, I doubt if it would ever be as widely used as either credit cards or paper money.















Another interesting item is this beautiful hologram coin depicting the renowned Angkor Wat.

Holographic technology is now commonplace in all sorts of financial instruments, from credit cards to gold ingots to paper currency. I wonder if we will ever see a hologram circulation coin one day?















And now for the most interesting part of the gallery - windows that let you take a behind-the-scenes look at how the Mint recirculates coins to keep the money flowing in Singapore.















Unlike the glitzy coin gallery, the production area looks just like any typical factory setting, with a bare concrete floor, big machines, conveyor belts and forklifts zipping back and forth.

Hardworking aunties and uncles sort through numerous bags of coins and prepare them for packing and recirculation.















The process begins when bags of coins are emptied into a big metal hopper.















Here's a hopper filled with one dollar coins - I'll bet that you've never seen that many "Kim Doon" (gold ingot: Hokkien slang for dollar coins) in one place before!















With the hopper loaded up, the auntie uses a continuous conveyor belt to sort through hundreds of coins, removing damaged or soiled coins from the pool.















Coins that pass inspection pour into another hopper of a giraffe-like machine.



















The machine then measures out coins in fixed quantities in order to wrap them into rolls of coins.















The coin wrapping paper gets drawn into the machine...















... and it spits out roll after roll of one dollar coins, tightly packed and ready to be sent to the banks for redistribution.

As a closing note I should mention that the Singapore Mint doesn't only sell collector's coins - they also sell "Singapura" gold bullion coins based on the daily gold price. Singapura gold is available in one, 1/2, 1/4 and 1/10 troy ounce sizes. Please enquire at the counter for more details regarding their products.


Would you like to know more?

Other posts about Singapore history:
- History Herstory My-stery