Thursday, December 31, 2015

The Brain, Basic Memory - Recognition

EEG cap
Probing the Brain

What are the mechanisms of human memories? A human memory is the playback of a perception, like the taste of sugar or the look of someone’s face. The mechanisms proposed here are a combination of naturally occurring feedbacks and equivalence. Such mechanisms do not involve storage and retrieval. For centuries theories about storage/retrieval, encoding/decoding in the brain have been unfruitful. The feedback mechanism here circumvents that and charts a new course to the mind.

Memory recall of past events can be specific or approximate. What did you have for dinner last night? where is Jerry's school? To answer correctly, one must make a conscious effort or it is just guessing. How do feedbacks and equivalence provide a way for specific recall? In this discussion specific recalls are actually more evolved. They depend on two additional mechanisms: adaptation and resonance. We will get into that when we go over sequential (objective) memories and associative memories. First, let us see how a feedback mechanism can explain the simplest type of memory - recognition.

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By Roberto Ferrari from Campogalliano (Modena), Italy
Wile E. Coyote Can Run On Two Legs Like People

Recognition, or re-cognition, is the replay of a perception. It is a perception that something similar or approximate had been experienced before. When a child watches cartoons he sees the drawn figures as people, even though the figures are only somewhat similar to actual persons. That is recognition. When Harry meets Sally, he has her name at the tip of his tongue. That is also recognition. When one eats Thai food and finds it similar to Chinese food. That is still recognition. Recognition has this trait - it is similar but not the same as the original cognition. To use feedbacks and equivalence to explain this evocation of prior experience, we need to first describe what are feedbacks and equivalence in the context here. Feedbacks here refer to IFP feedbacks, which are Impulse Firing Patterns (IFPs) going around from neurons to neurons and back. Neurons are nerve cells that can fire voltage impulses. The aggregate of these voltage impulses, relating to a particular sensory impression, is called a pattern, or an IFP.

Computer Simulation of Neurons Firing Impulses

IFPs travel spatially and change temporally. Inside a body, IFPs propagate along neural pathways, notably in the cortical regions of the brain where scientists scrutinize the most. Neurons in different regions have different numbers of synaptic connections and biochemical surrounding. These differences affect the outcome of the firings. The neuronal impulse firings can also change in response to the modulations of sensory inputs. Many computer animation clips show that impulse firings are sporadic and isolated. But that is not what EEG (electroencephalography) shows. EEG is a very coarse wiretapping of IFP, and its output is continuous and rhythmic.

EEG, ElectroEncephalogram, Records Voltage Variations from Impulse Firings

Outside a body’s nervous system there are no neuronal impulse firings, so therefore no IFPs. But metaphorically we say that IFPs can transform into patterns of physical actions and reactions that reach outside. For example, nerve impulses excite bodily actions such as arm and leg movements, facial expressions, or verbal communications. Those actions trigger responses in the environment such as people looking or cats running away. Those reactions trigger further reactions such as laughs.

Feedback In Nature Is Mutual Causal Interaction.
IFP Feedback Is Mutual Causal Firings

Then, at some point, some reactions reach back and catch the instigating subject’s attention. The subject’s senses thereupon fire up IFPs again internally in the nervous system. That IFPs travel up to the brain and trigger consequent internal transformed IFPs there. This circuit of propagation, or feedback loop, can be described as IFPs-inside-body to actions-outside-body to IFPs-inside-body and so on.

In such a metaphor, neural IFPs travel in and out of a body physically or virtually. Sinbad the Sailor did seven voyages in a tale of the Arabian Nights. In each voyage he disappeared abroad. Then he returned home, became a much changed man, lived a domestic life for a while, and then yearned to go overseas again. Just so, IFPs disappear outside a body, return back in the body, and then vanish yonder again. They go round and round and in and out. So too are all things that move in cycles in this world. Water, starting as an arbitrary drop somewhere, in a lake or a river or the inside of a living being, will travel away from that point of origin and come back again. Shifting the place of origin does not change the nature of circulatory propagation. They always transformatively exit from and return to the arbitrary point of origin. However, in the discussion of memory we do need an arbitrary starting point. The origin point can be at the nerve endings of the senses, or it can be in the cortical regions of the brain since that may be where perceptions are immanent.

IFPs Are Equivalent to Sensations/Actions

So much about the feedback part of IFPs. What is the equivalence part of memory? Equivalence here refers to the relation between impulse firing patterns (IFPs) in the brain and mental perceptions (MPs) in the mind. It is an inseparable co-presence of one another. On the one side is a physical formation of neuronal firings, and on the other a mental in-formation of perceptions. Where one exists, the other one must co-exist also. If an IFP takes place in the brain, a mental sensation is perceived by a person. Conversely, when a person has mental perceptions, his brain (or nervous system) is firing IFPs.

One notable example of equivalence is the phenomenon of gravity. Gravity was discovered by Sir Isaac Newton and studied by Dr. Albert Einstein. Newton pointed out that mass and gravity were equivalent. Wherever there is mass there is also gravity, and vice versa. The story was that an apple, pulled down by the mass of the Earth, hit Newton’s head while he was under the tree. The falling apple was a revelation to Newton. Because at that time he had been puzzled deeply by why the planets orbiting around the Sun elliptically without flying off in straight lines. He couldn’t have peace without an answer. Then the mystery was solved by the falling apple because the Earth was pulling it to the ground. Just so the Sun was also pulling the planets towards itself that resulted in elliptical orbits of the planets. And Newton called this revelation of massive pulling force Gravity.

Equivalence of Acceleration and Gravity

A couple of hundred years later Dr. Einstein pondered on the speed of light, and pointed out that acceleration and gravity are equivalent. In his theory of General Relativity he used an imaginary elevator to illustrate this. When one experiences acceleration in an elevator, that experience is indistinguishable from a weight or the pull of gravity. Both Einstein’s and Newton’s equivalences can be seen in the basic physics formula F = M * A, force equals to mass times acceleration. Newton emphasized the F and M part of the equation and showed that mass and gravity (force, or weight) were always co-present. Similarly Einstein picked the F and A part of the equation and showed that acceleration and force (gravity) were always co-present. Equivalence in this discussion simply means the co-presence of Items on different sides of an equation.

Einstein's Elevator

With feedbacks and equivalence, recognition can be explained this way. IFPs circulate virtually from the outside to the inside of a person’s body. They are feedbacks a person gets from the environment. Or simply, a person sees, touches, smells, hears, or tastes something around him. At the boundary of the body, these IFPs are triggered by the senses and then travel up to the brain physically. In the brain mental perceptions (MPs) take place as the equivalent of IFPs. These equivalences are called sight, feeling, odor, sound, taste. The first time these IFPs circulate in the brain a person has a cognition, or sensory perception. The second time similar IFPs circulate again along the same internal pathways, this person will have not only a cognition, but also a recognition. The second cognition reminds him he has a similar cognition before.

Why does the second circulation of IFPs make one know of a similar cognition before? The question has to do with what “knowing” is. We contend that knowledge is a mental feat based on memory. Knowledge-memory is an act of associating one perception to another perception, or a text to its context. The act of association can be done through feedbacks (and resonance) that allow triggering of one IFPs to or from another IFPs.

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By Dirk Beyer. A Buddha Statue in Kamakura

A young man once had an extraordinary experience. His friend went on vacation to Japan. The friend took some pictures of a giant Buddha statue near a temple. He came back home and showed the pictures to the young man. The young man’s eyes got wide open, “I have seen this Buddha statue before. I was there, but I have never traveled to Japan in my life! How could it be? Was I dreaming? Yes I think I saw it in a dream.” This is an example of what the French called Deja Vu. Many people have experienced deja vu. They remember seeing or hearing something, but find it very odd to explain how they saw it in the first place.

The recognition mechanism applies here. When the young man sees his friend’s pictures of the Buddha statue, he is having certain IFPs coursing through his brain a second time (IFPs 2). The first time was when he maybe dreamed about it (IFPs 1). (IFPs 1) has a seeing-the-statue part (IFPs 1-0) and a context: a dream (IFPs 1-1). Or (IFPs 1-1) is a perception of waking up from dreaming. Anyway, (IFPs 1-1) is the context of (IFPs 1-0). Or (IFPs 1-0) and (IFPs 1-1) are related in that they are sequential or concurrent plays of a streaming perception. So when (IFPs 2) is playing out in the brain, (IFPs 1-1, the context) is triggered to play back because (a) (IFPs 2) is similar to (IFPs 1-0), enacting in the same areas of the brain, and (b) the neural propagation pathways between (IFPs 1-0) and (IFPs 1-1) have not changed much. Now (IFPs 2) leads to (IFPs 1-1), and (IFPs 1-1) triggers a replay of (IFPs 1-0) by means of feedback (or resonance). The event sequence is (IFPs 2) to (IFPs 1-1) to (IFPs 1-0). This becomes recognition, or seeing-Buddha-in-picture leads to replay of seeing-Buddha-in-dream.

Actual Footage of (Partial) Impulse Firing Patterns

While IFPs are physical activities that can be partially probed and coarsely recorded as EEGs, MPs (mental perceptions) are informational phenomena that cannot be physically measured. They are information (text) that can be referenced by other information (contexts). The anthropologist Gregory Bateson defines information as a difference that makes a difference. MPs may be consciously known or subconsciously unaware. In the Buddha-pictures example, the context is remembered since it was a dream known consciously. So the recognition is lucid. Yet dreams are often forgotten. If a context is submerged subconsciously, then recognition can become fragmented. The taste of Thai food reminds one of Chinese food, but one may be vague about where the resemblance comes from. Harry cannot recall Sally’s name even though it is at the tip of his tongue. The context of hearing her name is yet to surface into Harry’s consciousness so possibly the subsequent recall of her name is buried as well. A child takes the actions in cartoon as actions of real people. Since human actions are imprinted into the child’s sensations daily. That become contexts for the child’s understanding of the cartoon. It is a false recognition.

Dr. Elizabeth Loftus Describes False Memory

False memories (recognition) in adults have been studied recently as a reality. In some cases criminal suspects are convicted by the testimony of eyewitness. Then it turns out that DNA testing or some other evidences exonerate the jailed convicts. It is not that the unwitting witnesses make up false testimony. But they sincerely remember something that was not what happened. The witnesses’ memory of the crime events prove to be faulty.

The psychologist Oliver Sacks has written a story about his own false memory that he is keenly aware of. The mystery of such false memory seems to be solvable. Studies show that false memories can be implanted by seeding questionable contexts into a subject. In the feedback model false context IFPs can trigger alternate firing of text IFPs, which become false memory. It is akin to a cartoon roadrunner being taken as a real bird, or Santa Claus being the real gift bearer. The meaning of the context is just as relevant as the meaning of the text. Without context, a text is a thing-in-itself (ding-an-sich), a magnetic monopole, an axiom of a treatise. It becomes inexplicable.

How To Implant a False Memory

One serious consequence of alternate contexts is political diatribes. One party accuses the other party of falsehood. Mutual accusations can go on and on ad infinitum because the two opposing parties insist on different contexts for an issue. The arguments will stop once they agree on a same context. So to bring political discords into agreeable discussions is a matter of harmonizing contexts used by the parties. That could be a wide open field of research in psychology.

FMRI scan during working memory tasks
fMRI Scan During Memory Tasks
Red Areas Indirectly Indicate Neuron Activities

Although IFPs are physical activities vital to memory, they are not yet visible. What do IFPs really look like? They take place among neurons. Some computer graphics videos show artistic renderings of individual neurons firing impulses. But the graphics do not depict the firings as a group nor in a sequence. The more advanced fMRI (functional magnetic resonance imaging) and EEG (electroencephalogram) pictures provide better but indirect glimpses into IFPs. But they are still like representing a 3D object in a 2D medium. Is there another way to see IFPs? Perhaps there are analogs in nature that may resemble IFPs. We can look for phenomena that share common characteristics. These characteristics must include (1) multiple similar active elements, and (2) actions / reactions among the elements in feedback loops.

Examples can be a school of fish fleeing at the approach of sharks, or weather systems instigated by the temperature gradients of flowing ocean currents. Additionally, individual branches of IFPs may resemble the path of lightning. But this is all incomplete and imagined.

Movement of Weather Systems May Resemble Movement of IFPs

One important note about feedbacks. In feedback loops, the presence of active systems is essential. Feedback loops are different from circulation loops in that their pathways consist of active elements instead of passive ones. Passive elements are pushed or pulled along. They do not have internal energy supply. When one billiard ball hits another one squarely, the second ball moves faster or slower depending on the momentum of the first one. Active elements are those that have their own energy supplies and react independently to the input’s energy level. Neurons have their own energy supply from blood. The response of neurons to impulse inputs can be to fire impulse output or to not fire, or to fire impulses that promote or inhibit other neurons’ firing. They make the interactive outcomes complex, unpredictable, and alive.

In simple or nested feedback pathways the overall IFPs are the aggregates of numerous individual neurons firing or not firing over the time period of an input event (and maybe beyond). Also, the neural feedback pathways themselves will change with the wax and wane of synaptic connections. That is an additional layer of complexity, a part of neuroplasticity. Some cortical regions are more developed than others, just like some body parts are more dominant than others, like a left eye or a right hand. The growth of brain regions is subject to economic / ecological forces, as the flux of IFPs can promote or reduce cortical blood circulation (for energy supply to neurons), and thereby indirectly stimulate or demote synaptic connections of neurons and perhaps even the number of neurons. “The rich get richer, the poor get poorer, a revolution resets all, then it starts over” is a generalization applicable to economics as well as to physiology. Both are systems of active elements interacting in feedback loops, subjected to positive and negative feedback controls.

Neuroplasticity Animation

While the magnitude of complexity of IFPs is gigantic, it enables the IFP-feedbacks model of memory to solve two problems that a storage model cannot. One is the question of how much a brain can remember. The storage model suggests that a human brain cannot store much. 100 billion neuron cells in a brain can roughly store 6 hours of DVD-quality sight and sound information. Since 1 DVD has about 4 GB of memory and plays for about 2 hours of audio/video, and one neuron can store 1 bit of information. Do we remember only 6 hours of sight and sound of life? Of course we remember more than that. The IFPs, however, being firing patterns of neurons, have far more combinations than the number of neuron cells. The combinations of impulse firing variations are on the order of 2 to the power of the total number of neurons in one time instant. Integrating all the instants when the input event occurs, the number of possible IFP combinations is on the order of (one instant combinations) to the power of (number of instants). Theoretically it is practically limitless how many firing patterns - or perceptions - can manifest in one’s brain, even though an adult human brain holds only 86 billion neurons on average, as found by Dr. Suzana Herculano-Houzel and her team.

The other question is where memories are located in the brain. The storage model requires specific locations be dedicated to memory. That was disproved by experiments of neuroscience. Patients who have brain operations can loose some memories due to some parts of the brain being removed. But later some of that lost memory will return as the brain heals. The feedbacks model can explain this because IFP feedback pathways in the brain are multiple and redundant, like tree branches. Neuron’s dendrites grow outward to form synaptic connections with other neurons like tangled vines. In such entangled network of connections redundancy of impulse pathways is normal, while singular IFP pathways are less likely because singular pathways come from environmental constraints. It is a specialization process that develops later.

Bush vine Uzbekistan 02.jpg
By Andrew Teubes, Entangled Vine, Similiar to Entangled Neurons.

In redundant circuits, if some routes of the pathways are blocked or lost, other regions can take over and reestablish the lost branches. Why is that so? The process is unclear, but it can be illustrated by the phenomena of body metabolism. The effect is commonly seen in healing and during growth. A child can regrow a new tooth when an old one is lost. A severed finger can regrow connective tissues if attached back in time. A familiar melody can be recalled in totality when only a few notes is played. They show that somehow some interactions, perhaps just by iterations of feedbacks, can reestablish missing parts and make it whole again. It is like recognition that can play back memories by feedback of context. Anyway, self-reconstructing missing parts of redundant structures is a natural phenomena. Trees do that when branches are broken off. The TV game show Wheel of Fortune is popular because everyone can play and win prize money by reconstructing blank words into full phrases.

By Fallerd. Missing Tissues Are Replenished As the Wound Heals

Finally, this theory of memory is based on the axiom of F.A.R.E. mechanisms - feedbacks, adaptation, resonance, equivalence. The F.A.R.E mechanisms themselves are not explainable, since the presumptions or axioms of theories are unexplainable by the theories themselves. The Declaration of Independence of the U.S. states that “.... We hold these truths to be self-evident, that ….”. That self-evident truths are unprovable presumptions. The mathematician Kurt Godel proved this oddity in his formal treatise the Incompleteness Theorem. Anyway, the F. and the E. mechanisms can produce recognition-memory, and they involve ambiguous similarities that lead to either false recognition or correct memory. An additional mechanism - adaptation (A.) - can produce faithful and consistent recalls. That will be the topic of sequential memory, which is also called muscle memory or objective memory. We will get into that later. Next we will examine some more examples of false recognition in order to be clearer about what similarities are when we talk about similar IFPs and memory.

Tuesday, September 15, 2015

The Brain, Definition of Memory

The evolution of neural circuits in the cerebral cortex follows the Hebb’s rule. They are not designed by higher beings to do specific functions, but are formed by reactions to environmental conditions. How then does this create memory and what is memory? The Merriam-Webster dictionary says memory is the power or process of remembering what has been learned. OK. Then what is the definition of “remember”? It is the process of recalling memory. Voila! a circular explanation. That may not be clear enough. So let us take a look at some characteristics of memory first.

Rashomon logo.jpg
Rashomon logo by Daiei Film Co., Ltd.

Human memory is not black or white like the computer memory. The Japanese director Akira Kurosawa once made a movie called Rashomon. It was a story of three witnesses - a woodcutter, a bandit, and a wife - recalling the murder of a samurai. Their first-hand accounts were heard by a priest and a commoner. But the accounts were so different from each other’s that the priest believed that some or all of them had lied. And the commoner said that men were always motivated by self-interest, and they disguised the truth to fit their needs.

The movies did not reveal which witness was lying. And the audience was left guessing what had really happened. Strangely or not so strangely, many liars do not think themselves as liars. They believe their version of the story is quite acceptable and not wrong. What if the witnesses at Rashomon actually all believed that his or her memory of the murder was the truth, despite contradictions from others?

Hidden Camera

Some businesses set up “hidden” cameras in commercial areas to record what is happening. This provides objective data for security purposes. In most private lives there is no such monitors. Without camera recordings there is only the witnesses’ recollections of an event. However, people’s subjective accounts of an event are always somewhat different because the human memory is a transform, not a copy, of their perceptions. The neural transformations can vary in many ways, so the memory recollections will also vary in many ways.

A math teacher goes in front of a class to talk about the distance formula of geometry. After the lesson, how much do the students remember the lesson? None, little, some, or most? Can even the teacher himself remember what has been said verbatim? Certainly not. The same applies to language lessons, movie viewing, conversation, travel, or all other activities. The Rashomon phenomenon happens not only at Rashomon, but at almost everywhere.

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EarthDATAsafe Haupt. Objective Data Store

However, there are objective truths. Or at least science and technology can demonstrate there are some. By classifying and analyzing carefully collected data, scientists can predict and control the properties of objects, and make our lives better materially. That is evidence of objective truths. In doing so, however, they also subject our human memory to objective data, making people think and act more and more like a machine.

Confining subjective memory to objective data has one advantage. It trains the memory to be more accurate relative to the objects in question. That makes the study of memory easier for scientists. The subjective memory on the other hand is not about accuracy but about imaginations. Story and art and playacting are disciplines that encourage imaginations. They let the mind roam free, using poetic license to play with objective truths. Objectivity is geared towards the material, while subjectivity is towards the spiritual.

Most basic skills are learned by training subjective impressions into memory that conforms to objective phenomena. Examples are reading and writing, dancing or cooking. Musicians like Pete Townsend or Paul McCartney had to practice long and hard before they could get their fingering right on the guitar. Rote learning comes from practice. And practice makes rote learning easier.

Repetition from rote learning causes neural circuits to form and solidify, per Hebb’s Rule. These circuits circulate impulse patterns that resonate to objective phenomena. Typing on the keyboard without needing to look at the keys is an “objective” memory. What about “subjective” memories? That might be neural circuits that circulate impulses between objective memory circuits, producing associations of various objects. For example, association of a flying carpet or a winged horse, or an owl talking to a girl lost in a forest. It weaves and fuse things together: carpet and sky make a flying carpet; owl and words make a talking owl; and human and swan make a ballerina figure in the Swan Lake.

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Book of Genesis Illustrations, God Created Man.
by Distant Shores Media/Sweet Publishing.

The book of Genesis in the Bible tells a story of creation. Genesis 1:27 says, “So God created mankind in his own image.” This creation is a foundation of Christianity. Invert this saying and it becomes “So mankind created spirituality in his own imagination.” That is like turning a subjective faith into an objective observation. We can see there are many religions in the world where people practice spirituality differently but we do not see God directly. In my imagination, subjective memories and imaginations are the outcome of “meta” neural circuits, something that are “read between the lines”. Although they too can become hardened circuits from repetition, which become personalities or mental traits.

Acclimating body to cold weather

So far it is only about brain memories, which can be classified into objective and subjective types. But memory is not confined only to the brain. Memory is in the body as well. Muscle memory is a common example of body memory. Athletes’ hands and feet and musicians’ fingers are filled with memory that are tuned to play what they have practiced to play. In most cases, brain memory actually interferes with muscle memory (dexterity) as the saying “thinking too much is not good” shows.

Furthermore, the skins and the glands have memory, too. A light-skinned person can get a tan by sunbathing. The tanned skin remembers to keep the darkened melanin around to absorb the harmful UV light. This makes the people living in sunny areas to stay dark. The skin not only remembers adaptations to the sun, it also remembers changes due to exposure to temperature, humidity, and air pressures. It is known as bodily acclimation to the environment. Unacclimated visitors notice very quickly the physical stresses of a new environment on the body, while the locals feel nothing. That is because a new comer’s body has not yet remembered the changes it needs to adapt.

Jonas Salk Congressional Gold Medal.jpg
Jonas Salk, inventor of Polio Vaccine,
Congressional Gold Medal -

The memory of glands can be exemplified by the immune system. When one gets sick and then recovers from a contagious disease such as the flu, one develops a specific immunity against it. At one point the white blood cells and the immune cells get to know the foreign viruses when the body is being sickened by them. The next time the same viruses come around, the immune cells eliminate them quickly by memory, without going through the sickness again. This body memory is how vaccine works. Polio vaccine was invented by Jonas Salk and consisted of dead polio viruses. Injecting polio vaccine into the body makes the body remember the viruses, so that the immune system will know how to eliminate live viruses easily in future infections.

DNA-split by US Department of Energy
- DOE Human Genome project.

Delving deeper, the genes of DNA are also memories. Passing on the genes from parents to children is how the children inherit the parents’ physical traits, such as the hair colors or eye sizes. However, DNA is a bundle of genes in sequence. The sequence is just as significant as the genes themselves. The individual gene is not a static code or mold of a specific physical trait, and DNA is not just the combination of all the traits together. The sequence in the DNA molecules shows that there must be a timely order for the unfolding or becoming of things. This can be seen in the combined DNA’s of a fertilized egg in the womb. The cell divides and then combines into a fetus, and physical traits appear along the way sequentially, not simultaneously. It is a memory playback of dynamic processes, not a static state. In other words, it is a memory of a development, not a memory of the outcome of a development.

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Ocean migration of Altantic salmon.

Perhaps an analog of this “process” memory can be seen in certain animal migrations. Adult salmons, after years of living in the ocean, somehow mysteriously remember to go back to the freshwater creek where they were born, repeating what their parents had done once upon a time. After returning back to their birthplace, most adult salmons spawn and die. Such a return-to-root journey happens only once in their lifetime. What, then, enables them to find their way back from the vast oceans in just one go? Some scientists propose that they find their way by sensing the Earth’s magnetic field. Maybe so, or maybe the migration is a late-stage memory playback for the fish. This late memory triggers the fish to start migrating. Along the way many fish gather together and a group dynamics take place. This group dynamics produce a group memory where each and every fish contributes to the migration path. The collective memory of the whole group directs them back to the river where they came from. It is like the neurons forming a neural circuit, and the neural circuit develops a resonance (memory) that directs the impulse firings of the component neurons.

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Re-circulation without the original seed.
Pollard's Rho Hash by Dake - Own work.

Anyway, with all the digressions on various aspects of memory, what is a better definition for it? The answer lies in the usage of context or reference. Our definition uses “circulation” (loop) for reference. So, memory is a re-circulation of a sequence of events, without the original trigger. For example, the brain memory is a re-circulation of impulse patterns in some neural circuits. An impulse pattern may start circulating by some stimuli of the senses. The senses are the relatively original trigger. If the same impulse pattern circulates in the brain again, and is not triggered by the senses, then it is a memory. The formation and presence of neural circuits can make impulse circulations definitive and repeatable. The repeatable impulse circulations are where we can examine memories objectively.

How do neural impulse patterns circulate? What impulse circulation pattern corresponds to what type of brain memory? That will be the topics next.

Sunday, August 23, 2015

The Brain, Neural Circuits

Do smart people have bigger brains? Some do but not all. And that is not what makes them smart. If it is, then all adults are smarter than kids because of the brain size. That is certainly not the case. Take Albert Einstein for example. Einstein was super smart but his head was not especially large. He figured out the theory of Relativity that no other scientist could. He also needed others to tell him his home address when he got lost. That shows that smart people can be dumb too, and vice versa!

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Margaret Mead, left, with Moshe Feldenkrais
and Karl Pribram - International Feldenkrais Federation.

The size of the brain or the number of brain cells plays only a small role in intelligence. Some people with normal brain size can be much smarter than average, like the anthropologist Margaret Mead. Besides, a small-brain creature can be smarter than its large-brain cousin. A fox can always outsmart a man playing hide-and-seek. And a man is smarter than a fox when it comes to talking and using tools. They are just smart in different ways, paying attention to different things.

Comparing the brain to the Internet. From Neurons to Networks.

Can a person learn to be smart? Sure. When one has learned to play music or do science, one becomes smart. Of course, there are people who are gifted and can pick up learning much easier than others. They are naturally talented. But that does not exclude nurtured smartness. Edison says that genius is 1 percent inspiration and 99 percent perspiration. One of the goals of education is to help the students realize their intelligence. How can that be achieved? The key is the neural circuits, especially the ones within the brain. The way to get there is to nurture neural circuits to observe and to remember.

Reuniões Conjuntas - VII Semana de Valorização da Primeira Infância e Cultura da Paz (15859576516).jpg
Suzana Herculano-Houzel, the scientist who counted neurons. Reuniões Conjuntas - VII
Semana de Valorização da Primeira Infância e Cultura da Paz by Senado Federal.

Neural circuits are made of cells in the central and peripheral nervous systems. The nerve cells, brain cells included, are called neurons. A Brazilian neuroscientist Suzana Herculano-Houzel and her team did an actual investigation on the number of neurons in the human brain. They came up with an ingenious way to count them accurately from 4 donated adult brains. The result was published in 2009. They find an adult human has about 86 billion neurons on average. That is fairly close to the conventionally cited number of 100 billion neurons. The number 86 billion is about the same from birth to death. Like retinal cells, the brain cells do not regenerate like other body cells do.

A Neuron

What is a neuron like? Each neuron has dendrites, a soma (cell body where the nucleus is), and an axon. Functionally, the dendrites and the axon are the receptors and transmitter of neural impulses respectively. The axon hillock part of the soma is an impulse generator. The axon endings (terminal bulbs) connect to the dendrites or soma of other neurons. The places where they connect are the synapses.

Details of Neuron

What is special about the neurons? A neuron is a cell that can receive and transmit electrical neural impulses, also called action potentials. The circulation of impulses is of main interest here. It can have feedback loops for control and differentiation. It is a basis for a theory of the mind. Neural impulses travel from the dendrites to soma to axon and then across the synapses to the other neurons. But it is not a straight passing through. There is a threshold gating involved in the cell body. In a neuron, if the sum of all incoming impulses exceeds a threshold, then its axon hillock (the soma/axon junction) fires an impulse down the axon to the axon endings. If not over the threshold, then it won’t fire an impulse. The brain has billions of neurons and trillions of synaptic connections. It is the propagation of impulses, their patterns and dynamic transformations, that will provide clues about the mind.

Where does the number of trillions of synapses come from? Probably from estimates of various studies. One Wikipedia article on neuron places the average number of synapses to be about 7,000/neuron. Others list the number from 1,000 to 10,000 synapses per neuron. Multiply 86 billion neurons by 1,000 you get 86 trillion synapses. But the number is probably higher since 1,000 is the lowest estimate.

Neuron Connection and Disconnection

When a baby is born, the number of synapses continues to grow. The number reaches its peak, estimated at about one quadrillion (1015), when the baby is 3 years old. By the age of 60 - 70, the number goes down to 100 - 500 trillions. Synapses can connect or disconnect depending on the situation, making neural circuits transitory (or stable) as a person grows and learns and changes. The changing synaptic formations surely affect our memories, which are not always the same from month to month or even day to day unless they get “refreshed” regularly. Changes of neural circuits create changes of impulse flows, and vice versa. Which lead to changes of memory.

Neural impulses can be excitatory or inhibitory. The two opposite types are significant for they can build up a regulation mechanism. The types depend on the neurotransmitters involved. Neurotransmitters are chemicals that move from one neuron to another across the synapses, thereby allowing the electrical impulses (action potentials) to cross over as well. A lot of illicit drugs such as cocaine and marijuana work by causing changes to the delivery of neurotransmitters. These drugs work wonders, temporarily, to users who wish to experience alternative perceptions. Also, problems associated with neurotransmitters are present in mental illnesses such as depression, dementia, or Alzheimer's disease.

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Post Synaptic Potential Summation by OpenStax College
EPSP - Excitatory PostSynaptic Potential, IPSP: Inhibitory PostSynaptic Potential.

Electrically, excitatory neurotransmitters increase action potentials while inhibitory ones decrease them. Glutamate is an excitatory neurotransmitter. Mono sodium glutamate (MSG) used in Chinese food is a hyper tasty seasoning. But it leaves a feeling of dull headache to some people. One possible explanation for this is that MSG acts like artificial neurotransmitters that overheat the neural taste circuitry. Bones are full of glutamates. And soups made of bones are naturally tasty.

There are many other neurotransmitters, most of them are inhibitory. Acetylcholine and GABA are ones, as are serotonin and dopamine. The variety of inhibitory neurotransmitters suggest that their roles in many neural circuits are to reduce the flow of impulses, like friction does to slow down a motion. This is a natural and necessary occurrence as decreed by Chatelier’s Principle. It says that a reaction always acts to counter the changes introduced by the instigating action.

Factoid: excitatory impulses go across synapses that exist between axon endings and dendrites, whereas inhibitory impulses go across synapses between axon endings and soma.

Yin-Yang by Nevit Dilmen

Why are there two opposite types of impulses? What can they do together that one alone cannot? One answer is that they make negative feedback control possible. The body engages in many homeostatic feedback controls: heartbeats and body temperature. To regulate certain actions or variables it is always necessary to have two opposite agents, one contracting and the other expanding, a yin and a yang. For example, driving a car requires two opposite actions - acceleration by gas and deceleration by brakes - to control the speed of the car. Likewise, excitatory and inhibitory action potentials are both needed to push and pull, so as to regulate the flow of neural impulses.

Looking at the big picture, the brain and the nervous system are parts of a circuit that connects a person to his environment. The five senses are the connectors that pick up outside information by resonances and transmit that to the inside. They convert optical, auditory, olfactory, gustatory, and tactile vibrations into nerve impulses. These impulses then move along the nerves cells to the brain. The brain itself is again a city of circuits where the impulses continue to transform and propagate. From the point of view of circulation, what is inside and outside of a body, the I and not-I, are connected circuits where information flows. A body does not sever the loop where information flows. And sense organs are like synapses where information cross over from one side to another. That corresponds to the Buddhist concept that all things are interconnected (informationally). It is just that in Buddha’s time there was no word for "information". The lack of concept for information caused the bodhisattvas at that time great difficulties in understanding the Buddha’s teaching about the mind.

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Donald Olding Hebb.

What is amazing is that since 1949 it was already known some of the neural circuits in the brain are dynamically formed, especially in the cerebral cortex. This was discovered by a Canadian psychologist Donald O. Hebb. He noticed that neural wiring could be directly affected by timing, by whether the firing of impulses in neurons are relatively synchronous or not. Basically, if they are nearly synchronous then synaptic connections may establish. If not, then the connections may dissolve. Specifically, If the firings of neuron A happen repeatedly just before the firings of neuron B, then A will likely connect to B if they are not connected before. Conversely, if the firings of A are not repeatedly happening just before the firings of B, then A will likely disconnect itself from B if they are connected before. This gives rise to the phrase “cells that fire together, wire together,” or “cells that do not fire together, do not wire together.”

Hebb’s finding becomes a foundation for the theory of neural circuits. It is called the Hebb’s Rule or Neuroplasticity. This rule describes a basic mechanism of how neurons connect together, and how the connections can bundle up into circuits. But how do neural circuits and impulse transmissions relate to memories, thoughts, dreams, fear, and love? So far it is still a mystery.

There is a hypothesis that may help to unveil this mystery. It is a hypothesis to answer the question why does the formation of neural circuits conform to Hebb’s rule? The answer seems to be economics. Economy exists in all interactive systems and is as powerful as feedbacks. Hebb’s rule is an outcome of economic forces at play. For example, It takes less energy for two neurons to fire impulses if they are wired together, because their total number of impulse inputs can be reduced. So by economic bonding the synaptic connections take place. Also, neural circulation of impulses can bring in economic or other benefits. The mind rewards the body with getting and absorbing food more efficiently. And it makes the body adjusting quickly to environmental stresses such as predators, temperature variations, shortage of resources, etc. These benefits in turn promotes further neural circuit formations for the impulses to circulate.

Combining Hebb’s rule and theory of feedbacks, we may guess that cyclic circulation of impulses can create and stabilize circuits of neural pathways. The excitatory and inhibitory impulses can set up negative feedback loops to stabilize the flow of impulses. Then the stabilized impulse flows can in turn mold the formation of neural circuits since the relative timing of impulse firings becomes more definitive. The formation of stabilized neural circuits attracts further regulated incoming impulses. This is like the evolution of any economy. It becomes a cycle of reinforcement in a positive feedback loop.

One example of positive reinforcement is capitalism. A capitalist uses money to invest in companies to make money further. In such a positive feedback loop, an unchecked capitalism applied in a society will differentiate the rich and the poor more and more by the ongoing economic reinforcement.

Neural circuits may produce smart or dumb results. And habit is like a kind of neural reinforcement that can harden these circuits. For example, a person forgets where he has left his keys, a dumb result. He lets that continue and becomes dumber and dumber in recalling where his keys are. His mind is set to forget the placement of this particular set of keys. How can he correct that? Only by somehow rewiring his neural circuits that are “forgetful”. That rewiring is what learning is.

Nature always finds its way to counter-balance. Positive reinforcements cannot go on forever. It will either break down or be stopped. That corresponds to a tenet of Buddhism: everything is impermanent. Take the 5,000-year Chinese history for example. It is full of revolutions or invasions that punctuate its dynasties and territories. Are these revolutions not a natural reaction to break up the economic and political reinforcements of the prior regime? A person’s life journey is full of surprising experiences that may punctuate his career. Are these experiences not a natural intervention to break up the mental reinforcements of his previous beliefs and choices?

Hebb’s rule indicates that the wiring of some neural circuits are a matter of nurture, induced by actions of the environment. How to apply Hebb’s rule to develop neural circuits that are intelligent or happy is of great interest to many. Some of that can be done already. This has been amply demonstrated by the psychological exercise of positive thinking and by the religious exercise of keeping faith. People who think positively or can keep faith are happier and more peaceful. It just works.

There are also synaptic connections that are a matter of nature, laid out by the expressions of DNA. These neural circuits are naturally hardwired to regulate heartbeats, sweating, reflexes, and other autonomic functions. They are not learned but innate. But even some of that can be “mastered” by cultivating overlay neural circuits. For example, some actors can voluntarily make facial tics or shed tears at will as if they are genuine involuntary reactions. More amazingly, Tibetan meditators who practice Tummo can control their body temperature. Their feats are mind boggling. Presumably this is done by nurturing secondary neural circuits on top of the primary neural circuits to achieve the desired physiological “miracle”.

Iceman Wim demos body temperature control.

Neural circuits can be transitory or persistent. The transitory ones correspond to short term memory. And the persistent ones correspond to long term memory. In the brain, stable and persistent neural circuits are what Richard Semon called engrams. Engrams are assemblies of connected neurons where the circulation of impulses is cyclic and therefore self-stabilizing. Ecosystems such as coral reef, tropical forest, and wetland share something similar to engrams. They all have living creatures circulating about and molding the habitat, making the structure stable. However, neuroscientists have a hard time locating engrams in the brain by experiment. They remove the brain tissues of some lab rats to see how that affect their memory. This mystery is that no brain region corresponds directly to any particular memory.

This problem is probably due to the notion that memory consists of bits and pieces stored somewhere. Although that is true for computer memory, it is certainly not so for human memory. Memory storage space is simply absent in our brain. To understand memory, we will instead consider both engrams and impulse circulation patterns together, not just engrams alone. It is like trying to understand a coral reef ecosystem by examining the corals and the movements of plankton, krill, and fish around the corals. Both the stationary corals and the moving sea creatures change and affect each other. The two of them together, like text and context, will provide a better picture for understanding.

The first human EEG recording obtained by Hans Berger in 1924.
The upper tracing is EEG, and the lower is a 10 Hz timing signal.

How good is such analogy? We can use the brain’s electrical activities as data for comparison. Sea creatures can migrate from one coral reef to another. Such migration is like the circulation of neural impulses from one engram to another. We can tap that data using EEG. EEG (Electroencephalography) is recordings of impulse voltages from electrodes attached the scalp. The EEG traces show that the voltage modulations around the head are roughly rhythmic but can also include transients. These modulations correspond to the marine creatures’ seasonal migration (rhythmic movement) and habitat dwelling/feeding/mating (transient movement). So the analogy is not too far-fetched.

With the vocabulary of engrams and impulse circulations, and the grammar of feedbacks, we are now close to having a language that can describe the human memory.

Thursday, July 23, 2015

The Brain, Anatomy and Evolution

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Brain, by Pearson Scott Foresman

M: We cannot see the mind but we can see the brain. To understand the mind, we can start by examining the brain from the outside for a broad view, or from the inside for a close view, and from the time side for a chronological view.

From the outside, the human brain has 4 regions: 1. the big brain (cerebrum), 2. the small brain (cerebellum), 3. the brainstem (midbrain + pons + medulla), 4. the interbrain (diencephalon, the region between cerebrum and brainstem, not labeled).

The cerebral cortex, or the outer layer of the big brain cerebrum, is what commonly pictured as the brain. But it is actually only part of the inseparable central nervous system that also includes the spinal cord.

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Nervous System Diagram by William Crochot.

The brainstem goes down and becomes the spinal cord. The spinal cord is inside the spine vertebrate. At each segment of the vertebral column, the spinal cord sends out spinal nerves that connect to peripheral nerves that branch out to nerve endings that connect to all the organs (heart, lungs…), muscles, and circulatory and gland systems (blood, hormone, lymph). The nerve endings at the skin give us sensations of outside temperature, pressure, itchiness, pain, and others. The other four sense organs (eyes, ears, nose, tongue) connect directly to the brain via cranial nerves without going through the spinal cord.

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Tree fern (Dicksonia antarctica) by Evelyn Simak.

P: I see it the other way around. Instead of the complex brain connecting down to the spinal cord and spreading out as simple nerves, it is the root-like peripheral nerves gathering together to become the trunk-like spinal cord, and then sprouting out a growth called the brain, like a bud coming out of a botanical branch that is rooted under the earth. The tip of a tree fern even looks somewhat like to a brain. This order of progression is similar to Lamarck's theory that organisms evolve up the ladder of complexity and organization instead of down to the lower rungs of simplicity.

M: Maybe there is something valid in what you say. We can always boldly assume, but need to carefully verify. Evolution of the brain is not straightforward like everything else. It’s hard to know what a pre-brain was like because of the punctuated equilibrium situation. In punctuated equilibrium, the transitions are step-like - changes taking place quickly and fundamentally. Birds evolved from pterosaurs, a species of the dinosaurs. But who knows what pterosaurs really looked like. You can hardly guess how a turkey’s head look like from its skull. So it is also hard to guess the evolution of central nervous system from the fossil skeletons. Besides, which ones are the pre-human skeletons anyway?

P: There is a YouTube video showing the growth of the city of Las Vegas from satellite photos year-by-year. Some comments say that it looks like cancer. That is what makes me think of the brain as a tumor growing out of the spine. I don’t mean the brain is harmful to the body like a tumor. Just that it is a phenomenal growth fueled by available resources. Some say the brain uses more energy than any other organ in the body. But the brain also helps the body to take in more food and energy and use them efficiently. So it is a square deal.

M: If the resource income is greater than the expenditure, then there will be growth. Cities can grow because there are jobs and economic opportunities that attract people to move in and stay. It is all about resource development and usage. How does the growth of brain help the body develop resource income and use that efficiently?
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Circular flow of income and expenditure
by Bureau of Economic Analysis (BEA), U.S. Department of Commerce

P: Are we talking about economics now? Actually, come to think of it, I do believe that economic advantages are what drive the brain to grow so large. The dictionary says ‘economics’ means laws of household, and ‘ecology’ is the study of environment. The prefix eco- is household or environment, the suffix -logy study, and -nomics law. I didn’t see how economics and ecology are related. But now I see that they are both about what is going on in an environment of inhabitants. Ecology describes how the inhabitants interact with each other hierarchically and establish qualitative relationships like predator-prey or boss-worker. Economics describes how the inhabitants trade with each other and build quantitative relationships like producer-seller or marketer-shopper. Anyway, it is a simple way for me to think of them.

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Cross section of jellyfish, by Mariana Ruiz Villarreal LadyofHats.

What is the economic advantage of a big brain? The economic advantage is that the brain can help the body get more food (and other things) than the body can without the brain. It does so by using information from the senses (eyes, ears, nose, tongue, skin) to control and coordinate muscular/gland activities, and thereby capture more food. Look at how the primitive humans hunted with weapon and in group, not to mention that they made tools and built vegetable garden or animal farm. That takes much coordination and planning from the brain. Simple living beings like the jellyfish don’t have nearly as much development and advantage. They have no brain, only some loose network of neurons around the skin and the digestive chamber.

Our spinal cord probably shares similar functions as the jellyfish’s nerve net. It gets sensory information from the skin and reacts in a primitive way, such as the kicking reflex when a knee is tapped, or the secretion of digestive juices when food is in the alimentary canal.

But with the brain comes into the picture, some of the simple reflex reactions can advance to more finely tuned secondary controls. One example is the autonomic nervous system. This is an energize/relax control system based on the nerves coming from the brainstem and diencephalon. The autonomic nervous system is to maintain homeostasis of organ functions like breathing, digestion, circulation, metabolic rates. It is a secondary control in the sense that it is indirect. Direct control can be nerve impulses causing organ to contract. Indirect control can be nerves stimulating endocrine glands like pancreas or adrenal glands to release hormones into the bloodstream. The hormones then reach the organs to induce muscular or biological reactions for holistic homeostatic balancing.

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PID Controller, by Arturo Urquizo.

Secondary controls are to help primary controls to reach the goal more precisely. They evolve later after the primary controls. So the brain comes after the spinal cord, which comes after ganglia, which comes after neural net like those in jellyfish. Speaking of controls, engineers often use PID controllers for precision process/plant control. PID stands for proportional-integral-differential. Proportional control is a simple primary control based on the current sensor datum. Integral-differential controls are complex secondary controls. They are based on the sums and the trend of sensor data. By controlling the trend of data history, a finer, more stable and less oscillating control is reached than simple primary controls. This may be the case of cerebellum, the little brain, which maintains body balance and coordinates motor movements with sensory inputs.

Towards the end of the cerebellum video, it shows a loop where nerve impulses travel around the motor cortex, cerebellum, and bicep muscle to actuate a motion. With our negative feedback loop model, we can describe how the movement control works. First, visual information sets a reference target position for the hand to move to. Then, muscle and vision give information of where the hand position is. The governor, whether it is the cerebellum or the motor cortex of the cerebrum or both, is acting on the difference of the hand position and the reference target position and minimizing that difference.

Negative Feedback.jpg

The governor iteratively moves the muscles to reduce positional differences between the limb and the target. This is the movement sequence a baby learns to get hold of something or to walk. It is a primary proportional control. To maintain balance while walking is a secondary control on top of the primary control. It deals with reducing the shift of center of gravity while walking. With practice a baby will develop muscle memories for such movements so he can do it without looking or paying attention.

The sequence of primary negative feedback control is also how the missile system works. A radar senses a target’s position and sets that as a reference position. Other sensors calculates the position of the missile and the difference between it and the target. The governor, a computer getting the sensory difference data, directs the missile in the direction of the target to cut down their positional difference, till the difference becomes zero and the target is reached.

Movement control can be based on vision or echolocation (bat, radar, sonar). A blind baby can learn to walk with a cane without seeing. So it can be based on the sense of touch as well. What is special is that practice can turn movement controls into muscle memory. And movement controls can have a secondary component that is to govern the trend of positional differences. It is the memory of trends that account for how Michael Jordan doing jump shots or Tom Brady throwing football. It is to aim at a (relatively) moving target by throwing the ball to a position not where the target is at currently, but to where it will be in the future by the trend of movements. That is a secondary control.

The cerebellum regulates body balance and motor movements. What about the big brain cerebrum, does it regulate the senses? After all, eyes, ears, nose, tongue all have threshold mechanisms that are controlled by the brain. It regulates vocal communication and the formation of perceptions as well. Sight, hearing, smell, taste, speech, body language are all manufactured in the brain. Whatever the cerebrum is about, the evolution of the senses/brain must offer some advantages (economic and otherwise) to the whole body so that the body can nurture in return the growth and specialization of brain/senses, thereby ensure the survival of both parts.

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Iguana parietal eye by SurreyJohn.

M: Speaking of vision, there may be a clue to the genesis of the eyes. That is the parietal eye. Some fish, amphibians, and reptiles have a parietal eye, or third eye, on their head. This eye is sensitive to light and can provide visual cues to the brain. But it is not functioning like the regular eyes. An 8-week old human embryo has a pre-brain in an exposed pre-skull. The skull roof, the parietal bones, has not formed yet. It will form later to cover up the brain. However, some species have parietal bones not fused together during formation, leaving an opening at the top of the head after birth. The parietal eye is located at that opening. Lizards, frogs, and lamprey eels have such third eyes.

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Human embryo 8 weeks by Anatomist90.

In fact, all human sense organs other than the skin are located at the cavities of the skull. This raises the possibility that the origin of sense organs in the head starts from some cranial nerves being exposed to the outside environment where the skull bones are not formed to enclose the brain and shut out direct contacts. If the brain is, like you said, the latest growth in the central nervous system, then these cranial nerves are extended from the brainstem. The brainstem grows out of the spinal cord. The spinal cord aggregates from nerves of the rest of the body. Somehow, the exposure of the newly formed cranial nerves to the outside environment might have started a differentiation process that ended up as sense organs and the brain.

Actually, I think that is a good possibility. To illustrate this differentiation possibility, let me use a story of some explorers discovering an uninhabited bay that is filled to brim with fish and sea creatures. People hear about this discovery, so a few of them come and settle here to harvest the fruits of the sea. The bay is so abundant that more and more people arrive. And differentiation begins to go into high gear. The bay becomes lined with fishing boats and fishermen. Behind the bay grows mixed population and buildings and interlocking businesses. They pop out like mushrooms, serving the needs of the fishing industry and the community. And it keeps growing and differentiating until the whole place and interactions are stabilized. In this analogy, the explorers are the exposed cranial nerves. The bay is the outside environment. The fishing boats / fishermen are the sense organs. The bay area community growths are the morel-like cerebrum and cerebellum.

This story is like conjectures made by detectives to piece together clues to reconstruct what has happened at the crime scene. It is not the truth, but it may be a possibility that can lead to other possibilities that are closer to the truth. Anyway, how can some exposed nerve cells evolved into sense organs like the eyes? Well, it can possibly happen by a differentiation process of positive feedback or schismogenesis. What that positive feedback process needs is a difference as the trigger, and a circuit of active systems that can amplify and feedback that difference mutually and continuously.

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Positive Feedback leads to Differentiation.

The contact between the nerve cells and the outside environment can introduce such a difference. Einstein’s thesis on the Photoelectric Effect shows that light quanta can induce electric conduction in unconnected metals. In the absence of light, unconnected metals cannot conduct electricity. By this photoelectric effect, nerve cells closer to the outside light source can have a different electric impulse conduction than the nerve cells behind them. This photoelectric difference may be the trigger. And even if the photoelectric effect has not made the difference, then some other yet discovered factor(s) must have, since all living things exposed to a new environment do undergo changes. And those changes can lead to other changes, and on and on till stability is reached.

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Brain Vesicle Development Differentiation by OpenStax College

Once a difference exists, a positive feedback mechanism can start to enhance and reinforce it, provided that energy supplies are available to the systems to keep the feedback loop going, and the difference feedbacks do not reach the level of saturation or system fatigue. The spinal cord nerves are surrounded by nutrients-rich blood vessels. Blood cells are even made in the vertebrate bone marrow! That takes care of energy supply for the feedback systems. In the analogy of a bay turning into a fishing village, resources are pouring in to make the fishing technology more specialized and complex for greater harvest yield, along with creating a growth of people and accommodations and organizations to service the fishing technology. If a similar economic advantage holds true in the evolution of eyes, then nourishment would have made the exposed nerve cells more efficient at being photoreceptors, while also created growth of additional nerve structures such as brain lobes to service the information coming from the photoreceptors. Anyway, economic advantages of having sharp sensors are self evident. Look at the spies of the CIA or the Wall Street. They are highly specialized sensors in the ecology of national security or the stock market.

I agree with you that the evolution of senses is directed by economic advantages and differentiation. Or at least partly so. The economic advantages lie in the ability to perceive and to respond to changes in the environment. Sense organs are the first step to establish connections between the outside world and the inside organs. The connections have stimulated more neural growth to handle perceptions and responses. That goes on at the cell level in the brain as well. They are synapses of the neurons, which are what we will look at from the inside.

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.

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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.

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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.

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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

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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.

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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.

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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.

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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.