Tuesday, June 30, 2015

Sensors, Differences, Resonances, Information

Regular passive resonance.

P: So how are active sensors related to active resonances? And how is active resonance different from regular resonance?

M: Let us take a look at resonances first. Regular resonance is sympathetic vibrations of two objects. One vibrating tuning fork placed near another tuning fork will make that fork vibrate and produce a same pitch tone. That is regular resonance. Most musical instruments depend on regular resonance to make sounds. Active resonance differs from regular resonance in that the active one has its own energy supply while the passive one hasn't. Also, an active resonant object produces a transformed vibration pattern, not a copy pattern like the regular resonator. Powered microphone is an active resonator and sensor. It resonates to sound waves and produces electric waves. Cybernetically speaking, active resonance is one of the activities in the brain circuits. The other activities are feedback and adaptation. Together with equivalence, these physical brain activities can be mapped to memory and other non-physical phenomena of the mind!

P: Hmm, that is a bold claim. We will see how you will explain that. Where do you get these information?

Radar operation, uploaded by Averse from de.wikipedia.

M: From the history of technology. I was fascinated by war and technology. Before WWII, the Allies and Axis powers both needed sensors other than people to detect and track the movement of enemy aircraft. And radar (radio detection and ranging) was invented to do that. Radars proved to be such a success during WWII that resources were poured in for more research. From radars came radical advances in the understanding of negative feedbacks, also known as stability control and cybernetics. From negative feedbacks came the understanding how the brain acted as the stability governor of body metabolism and movement. Then robotic technology followed and grew like weeds. However, despite advances in robotics and computers, scientists still can not figure out how the brain works internally. The missing pieces are how or what information is circulating in the brain in regards to language and memory and dream and all the psyche stuff. We only know that electrochemical impulses are moving from neurons to neurons, and neurochemicals affect the impulse propagation.

Sensor Diagram.jpg
Sensor Diagram: Input, Threshold, Difference Output.

P: I hear that there is a big national project going on called the Human Connectome. It is to map out the complete wiring diagram of neuron cells in the brain. Anyway, where is the resonance part in your sensor diagram? It shows only that a sensor is a comparator that outputs the difference between a feedback input and a threshold reference.

Human eye cross section detached retina.svg
Cross section of a human eye, showing a detached retina at top.
by Erin Silversmith.

M: Let me use the eye as an example of an active sensor. The retina of the eye is lined with dense optical nerve endings called photoreceptors that connect directly to brain cells. Resonance? These nerve endings will fire up neural impulses as a resonant response to color variations, brightness contrasts, and location movements. It is an active resonance powered by nutrients in the blood. The neural impulse firings are a transformation of the optical information, not a copy. And the direction of resonance goes only from optical to neural, not other way around. The eyes do not emit bright light from the neural impulse firings of the brain, even though some pictures of animals might seem to suggest that.

Kattenretinatapijtweerkaatsing, Cat's retina reflection

The light seen at the eyes of animals at night are really only reflections at the retina. 'Bright-eyed' does not mean the retina is shining from within, just that a person is alert or eager. However, the sense organs are mood organs. We instinctively gauge someone’s mood by the look of his eyes or the tone of voice. Not only that, it can also be the flushed face, pricked ears, crinkled nose, etc. Body language is not a transformation from neural impulse firings to light or sound or smell, but to movements of muscles and body fluids.

Eyes, ears, nose, tongue, and skin are all sensors of active resonances. They produce waves of neural impulse firings to the vibrations of auditory, olfactory, gustatory, and tactile differences. In other words, they resonate to formations from the outside world, transform them into other formations, and transmit that to the brain. They are like antennas along the looping pathways of information. And information is in-formation, or that which is inside a formation. Formations like light vibrations or sound vibrations. Information is also en-formation, a formation that can trigger another formation. The word root 'en-' means to make, to cause, as in en-able and en-act.

P: Okay, enough of word roots. I see the difference output of the sensor in the diagram corresponds to your resonance. What about the threshold reference, why the difference of the input and the threshold?

M: Difference is the basis of information. Optical waves and appearances are themselves patterns of repeating differences. And these differences are further separated by a blocking threshold in a sensor. The threshold of our eyesight is partly set by the pupil. It dilates or contracts to adjust how much light can get onto the retina. The different amount of light that gets in is transformed to neural impulses at the retina. Then, on the pathways towards the brain, the opto-neural impulses are subject to another threshold adjustment. The brain has neurons that loop back and synaptically connect to these pathway nerves. The synapses get inhibitory or excitatory feedback impulses from the brain, which dampen or strengthen the transmission of optical information from the eyes to the brain. The thresholds are there to enable sensory adaptations to environmental changes.

When you walk from a dark movie theater out into a sunny place, you get too much light too quickly and cannot see well. But with the help of inhibitory impulses along the optical nerves, the intensity of optical information is reduced quickly and we regain the ability to see well. Similarly, changing from a bright to a dark place, we are blinded temporarily by too high an inhibitory impulse threshold set previously. Then, the brain lowers the inhibitory threshold, and we can see well in the dark place again. It is basically a negative feedback mechanism that regulates stable visual information flow, correcting either over or under transmission.

Fish market Jagalchi Busan.jpg
Fish market Jagalchi Busan.

The same kind of sensory threshold adjustment takes place in hearing, smelling, tasting, and feeling also. People who visit a fish market are at first overwhelmed by the fishy smells, but soon got over it. Those who love spicy Thai foods were at first stung by the powerful peppers. Gradually their taste buds acclimate to and build up tolerance for that. In the hi-fi world, there are audiophiles who spend thousands of dollars or more on loudspeakers. They believe that the speakers will sound better after a break-in period. Many hear a difference before and after, and swear that it is due to the mechanical break-in of the speaker components. But in fact it is the brain-ears thresholds that get fine-tuned and adapted to the speaker’s sound.

If you take the sensor diagram and relabel it as a governor diagram, it still sort of fits. Input, threshold, and resonant difference output are also part of the governor circuitry. Although what constitutes threshold and resonance in the brain will have something to do with memories, or learning, as they are closely related. We will get to that when we examine the brain circuitry. How the brain sorts out attractive differences and repulsive differences is more by learning than by genes. Suffice it to say here that mental threshold is sometimes known as bias or prejudice or preference. It blocks off certain information from reaching the governor, the logic, part of the brain. Tell a story and ask people to repeat it and see what happens. They will come up with versions that differ from one another as they have different biases. The Internet viral story of 'what color is this dress?' is an example.

Youtube, 41K+ comments

We all have our biases but we don’t like other people having them. We call theirs narrow-mindedness or tunnel-vision. And we call ours common sense or self-evident truth. Scientists have another name for bias. They call it presumption. And smart is the one who notices his own biases as presumptions. What may be a presumption? ‘What is heard is what is said’ is a presumption.

P: God knows how some people don’t listen. I myself sometime cannot hear the intention behind what other people are saying, or miss parts of what they actually say. Okay, I get what you mean by threshold. Anyway, music reminds me of dancing. People dance to music. Is that an example of active resonance?

M: Sure, dancing is a good example. And singing too. Active resonance is like imitation. The body moves to imitate the beats. The voice rises and falls to imitate the melody. Some are afraid to dance or sing because they feel awkward. Maybe it is because some mental threshold is blocking the urge to imitate? Little kids sure like to dance and sing without such inhibition.

Active resonances. Instrumentals start at 11:20

There is a band called the Grateful Dead. They play rock-n-roll music in a way that resembles jazz improvisation. When playing the instrumentals together, these guys listen to what the others are doing and groove with that. Each time they play a song it comes out very differently as it is a group dynamics. They show what feedbacks of active resonances are like.

P: I know this band. They are a famous hippies band during the 60s and 70s. Are we talking about 'expanded consciousness' or drugs here, the 'Summer of Love'?

M: We are talking about music and resonances here. Music and expanded consciousness do go well together. And speaking of hippies, some of them did do drugs, but some of them also studied psychology and spirituality, especially the Eastern philosophies such as Buddhism and Hinduism. Buddhism in particular talked about the sense organs and the mind.

Many Buddhists memorize the Heart Sutra (般若波羅蜜多心經). Here is an excerpt of that: “... No eyes, ears, nose, tongue, body, intention. No sight, sound, smell, taste, touch, dharma...” (original Chinese text: 無眼耳鼻舌身意, 無色聲香味觸法) There are two things of interest here. One is the word ‘no’ (無) and the other is the correspondence of sense organs and sensations. ‘No’ (無) and ‘emptiness’ (空) are two words used often in Buddhist sutras. Their meanings are puzzling yet mesmerizing to students of Buddhism. It is fascinating to hear how Buddhist masters and religious teachers past and present explain the phrase ‘no eyes, ears, nose…’. These sense organs and sensations clearly exist but the text says otherwise. The masters may not explain it but tell the students to meditate on it. Either way, nobody has gotten very far in making the text sensible whenever they try to communicate about it.

The five organs eyes, ears, nose, tongue, skin give us five kinds of sensations - sight, sound, smell, taste, and touch. That is obvious. But there is a sixth correspondence in the text: intention (意) and dharma (法). This is the interesting part. Dharma was taught by the Buddha and recorded in the sutras. Did the Buddha classify ‘intention’ as an organ and ‘dharma’ a sensation as the context suggested? Or was it just an inadvertent use of composition for the sake of including ‘dharma’ in it? Anyway. dharma = 法 (law) is a clever phonetic translation from Sanskrit to Chinese. Just as 'samadhi' translated to '定' (steadfast, stillness) is a clever phonetic play of language. But this cleverness actually mislead students away from the original meaning, which the Buddha said in the Lotus Sutra that only another Buddha could understand it. Well, when we build up a language for the mind we will see about that. From 500 B.C., around when the Buddha was born, to the middle of 20th century there was no such language. So it is no wonder that the dharma was hard to understand, and the Zen school had abandoned language and used meditation instead as a means to reach enlightenment.

P: Okay, this is getting exciting. Are you ready to build up a language of the mind, or memory, as we originally discussed?

M: Yes, just one last thing and we will get to it. We already have a few vocabularies for it - Feedback, Adaptation, Resonance, and Equivalence, F.A.R.E. You can spell it F.E.A.R. or R.E.A.F., however you like. But I want to mention a Zen Koan (禪 公案, zen story) first before I forget.

Zen. Which is moving? At 7:30

It is a story about the Zen master Huineng, told in the Sixth Patriarch Platform Sutra (六祖壇經). A flag is flapping in the wind. One person says, look, the flag is moving. Another person says, no, it is the wind that is moving. The sixth patriarch Huineng, before his identity is known, says it is not the flag nor the wind moving, but it is the heart (mind) moving. One Buddhist audience is taken aback and realizes he is a master.

In my language of resonance, it is the flag resonating to the movement of the wind. The eyes resonate to the sight of the flag movement, The brain resonates to the impulse firings of the eyes. The talking mouth resonates to the neural impulse waves of the brain. It is a circus of resonances.

P: Ha, a circus! Okay, let us talk about the brain now, shall we?

Tuesday, June 16, 2015

Positive Feedbacks Part 2, Permutation

Salat pao street vendor chiang mai 03.jpg
Salat pao street vendor Chiang Mai, by Takeaway.

P: I noticed something the other day at the Trader Joe’s store. There are 10 different kinds of frozen pizza in one aisle.

M: Yeah, and there are more at Safeway. They do it to give more choices to consumers so they can sell more. Do you know how all those varieties are created? It is done by combining similar ingredients in different ways. Food combination was not always common in the culinary history. The early humans ate herbs, meat, and cereal separately. One day they accidently mixed meat and herbs together, and that was a breakthrough in the discovery of tasty bites. The Chinese bun, BaoZi 包子, has meat and vegetables wrapped in a layer of dough. This combo invention was wildly popular. Imitations soon followed. It is possible that imitations of BaoZi include egg rolls, burritos, sushi, shepherd’s pie, sandwich wraps, or even Middle Eastern shawarmas, as they all share a similar structure. The magic of combinations has created new looks, smells, and tastes that people love. Look at the upscale restaurants. Nouveau Cuisine is also about combinations, with emphasis on simple and fresh ingredients.

P: Come to think of it, it is not only about foods but clothing and more. The variety of dresses, hats, pants, are created by combinations of some fabrics and shapes. I don’t know how Mozart composed his music or Van Gogh painted his pictures. But presumably they did it in part by creative combinations of elements of their respective arts.

Dimethyl-glucosylamine miguelferig.jpg
Organic Compound, by miguelferig.

M: Well, those are man-made stuff. Look at what Nature has. The combinations of four elements - carbon, hydrogen, oxygen, and nitrogen - make up organic matters that are the building blocks of lifeforms. From those combinations come sugars, fats, amino acids, proteins, cellulose, DNA, cells, tissues. Isn’t it amazing that myriads of living things have in common four elements: C, H, O, and N? That is probably why organic chemistry textbooks are so much thicker than the general chemistry ones. Because C-H-O-N combinations can far outnumber the finite properties and reactions of inorganic elements.

P: Organic chemistry is also about plastics and petrochemicals. I read a magazine story that says a lady in 1990s had tried to live without plastics for a week but couldn’t do it. Strangely, the combinations of organic elements remind me of the I-Ching hexagrams. They both are about combinations of simple elements.

Diagram of I Ching hexagrams owned by Gottfried Wilhelm Leibniz, 1701.jpg
Diagram of I Ching hexagrams owned by German mathematician Gottfried Wilhelm Leibniz, 1701
by Unknown - Perkins, Franklin. Leibniz and China: A Commerce of Light. Cambridge: Cambridge UP, 2004. 117.

M: Yes, that is so. The hexagrams are composed of six yao (爻) lines. Each yao line is either a solid line (yang 陽) or a broken line (yin 陰). So a hexagram is a stack of 6 yin-or-yang lines. There are 26 = 64 hexagrams. Each one has a name, and is a symbol for some phenomenon. For example, the fourth hexagram, Meng 蒙, is a symbol for not knowing and possible learning. Hexagrams are really permutations instead of combinations because permutation is more specific. One yin and five yang lines are one combination. But this combination has six possible permutations. What is mysterious about the I-Ching is how the ancients discovered or interpreted the elusive meanings behind each symbolic hexagram. How come this divination device worked so well in China? What is more, the principle of combination is also in many other fortune-telling devices: tarot cards, astrological charts. You can even create your own deck of tarot cards if you can cook up some new symbols and meanings.

Xiantianbagua 8 Trigrams, by Philolo.

P: Okay, what about diversity by permutations? Can you do that with your positive feedback loop?

M: Yes I thinking so. A positive feedback loop has two active systems, both amplifying attractive or repulsive differences. Permutations can be arranged on the sensory differences. Adding more systems allows more sensory permutations and more diverse relationships. For example, one permutation can be that the two systems amplifies different types of differences. One system amplifies attractive differences and the other repulsive differences. Such arrangement will be like a celebrity-paparazzi relationship. The star is repulsed and wants to get away from the paparazzi’s camera to protect privacy. And the paparazzi is attracted and wants to get closer to take pictures. This is similar to stalker-prey relationship. Wolves hunt deers. Ex-boyfriend follows the girl who wants to be left alone. I don’t know if parasite-host relationship is also this way, but at least one side is willing and the other not. Hunting and stalking are cruel, but they are also part of Nature.

Jongensspelen 10.jpg
Jongensspelen, chaser and chasee
by Anonymous - Jongensspelen. H.A.M. Roelants, Schiedam ca 1860-1870.

P: Okay, so a loop of one attractive system and one repulsive system makes up a chase-and-run relationship. How about if one system senses both repulsive and attractive differences? Is that a possible permutation?

M: Hmm. That would be like that system is having a mood swing. I can think of a yo-yo dieter in that kind of situation. He is at first attracted to the idea of diet and tries it. Then he is repulsed by the hardship of dieting and lapses back to overeating. After having gained weight he is again attracted to having a diet and thus back to square one. And so attraction and repulsion alternate in his mind.

The story of Hamlet by Shakespeare is another example of this. The prince of Denmark wailed ‘to be or not to be, that is the question’ as he pondered revenge to his father's death. In English there are words such as ambivalence, dilemma, and bipolar disorder to describe the various intensity levels of such mental (mood) swings.

David Garrick in Hamlet, Act I, Scene 4.JPG
David Garrick in Hamlet, Act I, Scene 4.

The chemistry Nobel laureate Prigogine is known for his study on dissipative structures, which start with a critical phase transition (e.g. water boiling). During this critical region a structure is alternating between two phases (e.g. water and steam). Such alternation is similar to mood swings during puberty and menopause, which are stages of transition. Risky choices are common during crisis, which is also a stage of transition. The Chinese word for crisis is 危機 (danger-opportunity), denoting that it is a fork to danger (危) and to opportunity (機) . To fight or to flee? To commitment or not to? To cover up or to be honest? Assessing hard choices is clearly stressful to the body as it copes with the mental swings and leaves dis-ease marks such as headache, ulcer, insomnia, irritation. This has prompted the rise of an industry called public relation or propaganda. Its service is to pacify the agony of hard choices by drawing attention to only one of the alternatives, for the sake of both the decision maker and the recipients. One glaring example of propaganda is the U.S. President Bush’s and U.K. Prime Minister Blair’s declaration of the threat of Iraqi weapons of mass destruction as they built up a coalition to invade Iraq in 2003.

What about the second system in the positive feedback loop? The second system can react to the oscillating first system by acts of propaganda. Or it can police or medicate the first system to reduce its oscillations. However, the second system cannot be indifferent to the first system’s changes. Because then the positive feedback loop is broken by the inaction.

Propaganda, policing, or medication are highly evolved devices that aren’t likely to be in the arsenal of the second system. A more likely scenario for the second system is that it reacts to the oscillations of the first system by itself oscillating. So in this permutation both systems are oscillating, although not likely to the same rhythm or melody. How do you call this type of oscillate-oscillate relationship? A dance, a resonance, a game?

Active Resonance - Flashdance
by Голубев Роман(ЛУЧШИЙ ВЕДУЩИЙ).

This game relationship is seen in all sorts of interactions. Examples are parents going nuts over teenagers’ erratic behaviors. Or bystanders dancing to the music of street performers. Or fish (or any animals) joining each other in unified yet irregular herd movements. It can also be police clashing against street protesters, opposing troops fighting in the battlefield, sports teams dueling on the scoreboard. Much studies on game (war) plans have been done to manage conflicts. Because each system can be lead to triumph or defeat, to joy or agony, to order or chaos, temporarily. Anyway, the outcome of such active systems resonances is unpredictable, like the butterfly effect on a game.

A tornado of fish.jpg
Active Resonance. A tornado of fish
by Bare Dreamer - Flickr.

P: Resonances of active systems? Hmm. Anyway, I wonder what is the basis for positive feedbacks. You mentioned that negative feedback is natural like the Chatelier’s Principle. But why is positive feedback naturally occurring?

M: Active resonances are closely tied to active sensors. That is an important basis for my sleuthing. We will get to that more later. Why are positive feedbacks naturally occurring? It seems that the cause is circular. Organizations (relationships, systems) arise from positive feedbacks, and positive feedbacks come out of organizations. I can say that since organization is natural, so positive feedback is also natural. Some people may not like circular reasoning. But I think it is a fundamental truth that things and reasons are circular in the biological world. The word ‘parents’ is meaningful because of the word ‘children’, and the word 'children' is meaningful because of the word 'parents'. What is the ‘left’ without the ‘right’? And what is the ‘right’ if it is not referenced to the ‘left’? Non-circular reasons are good for the inorganic fire and rock, the world depicted by the mathematics of Newton and Einstein. But non-circular reasons do not work in the circular biological world.

So how did positive feedback begin before there was any organization? That is a good old chicken-or-egg question. My guess is that it started with matters. Somehow it became possible for some matters to store energy (food). That turned those matters into active matters. In engineering terms, 'active' means that something has its own supply of energy for action. Whereas 'passive' means that a system depends on some other’s energy to react. We have talked about natural formation of loops before, like the water cycle. So together, a loop of circulation with two active units in it. That was when a positive feedback began to take place. Each active unit has stored energy for it to act on the feedback from the other. With this feedback loop diverging organizations emerged, followed by more complex positive feedbacks from the new organizations. It’s like two people A and B. A borrows money from B to start selling goods or services. B lends money to A to earn interests. As the money changes hands back and forth between the two, a positive feedback loop is formed as a business-finance partnership. A evolves into a store owner, and B to a banker. And they will continue to evolve to something else unless a negative feedback is established to stabilize their relationship.

There is a theory called Punctuated Equilibrium. It is an amendment to a problem in Darwin’s evolution theory. By mutations, competitions, and natural selection, the evolution of species should take place continuously over geological time. But that is not what is found buried under the earth. The fossil records show that the pace of evolutionary changes are step-like instead of gradual. Living species went through long periods of time with very little change (stasis, stability), followed by short periods of time with big changes (schismogenesis, instability), and then back to long periods of stasis again if big changes did not make them extinct. Paleontologists Stephen Jay Gould and Niles Eldredge noticed this and reported it with their theory of Punctuated Equilibrium.

Punctuated-equilibrium IT.svg
Comparison between phyletic gradualism and punctuated equilibrium (Italian)
by Miguel Chavez, modified by SunOfErat.

With our feedback loops model, we can say that punctuated equilibrium is due to both positive and negative feedbacks at work. The long stasis periods of the mostly-similar fossils correspond to a time segment where negative feedbacks overpower positive feedbacks, so stability predominates. The short schismogenesis periods of the changing fossils correspond to a segment where positive feedbacks dominate over negative feedbacks, so transformation prevails.

We can shrink the time scale and still find this dynamics. The 4000 years of Chinese history is a series of dynasties. Each dynasty has about 200 - 400 years of stable regime. The transition from one dynasty to the next is a time of increasing revolts or invasions, lasting about 10 to 40 years. From one dynasty to revolution to the next dynasty, that is also a form of punctuated equilibrium.

A human life span is about 80 years. Childhood, adulthood, and senior-hood are relatively long and stable periods where the body doesn’t change much. But puberty and menopause are short transition periods where the body undergoes major changes. A U.S. President is in office for 4 or 8 years. During this time the government has a stable administration. Then comes the next election and campaign of some months. That is when the stability of an administration is punctuated by calls for change. There is a Chinese phrase that alludes to this phenomenon: Ten years on the east side of a river. Ten years on the west side of a river. 十年河東 十年河西. It means impermanence. By adding the crossing of a river, which presumably is much shorter than ten years, this phrase will match right on for punctuated equilibrium.

P: Okay. That is too much information. My mind cannot handle any more of these permutations. Anyway, we started by talking about memory. How do you use positive feedbacks to explain the mind or memory?

M: Well, Positive feedback loops alone are not enough to explain memory. Let us first take a closer look at the sensor / governor components of our active system. There is this resonance phenomenon that needs to be brought up. Then we will get into the circuitry of the brain and see how memories are formed there.