May 17, 2015
JBT - Jim Blake thought or theory
JBQ - JB question
JBE - JB experiment
JBN - JB neologism, new acronym
JBN - I am hereby retiring the term “Junk DNA” there is no such thing, henceforth Junk DNA will be called Accessory DNA or simply ADNA. Note that the “A” is capitalized, ADNA is not “junk” at all. It is very important. This DNA was named “Junk” in the genomic dark ages 20 years ago. The age of the genome is no longer dark thus ADNA rather than “junkDNA”.
JBN - Genes carry the fundamental instructions, secondary cell function is carried out by post translational modification to both genes and the histone proteins they wrap and unwrap around. These modifications have many names: methylation, acetylation, ubiquitination, ADP ribosylation, citrullination etc. Henceforth these will be called PTMs. They will be referred to often throughout this essay. They are vital to life. they are now the key mechanism of Natural Selection as of 150 million years ago genes are finished evolving now evolution is left to PTM. Epigenetics is carried out by PTM. Epigenetics is the active key to all living things. Think of DNA as our founding fathers and epigenetics / PTM as elected leaders doing the daily work of government.
There are many plant species, worms, birds and reptiles that have larger genomes ( more genes that code for specific proteins) than humans but the proportion of an organism’s ADNA is in direct proportion to species complexity and of course humans have the most ADNA in our genomic trunk with 98% of our DNA non-coding for protein. We play a few genetic notes at each cell type but we do so with great feeling, like B.B. King, famous for playing in a small box or two of notes the guitar neck but to tremendous effect. How did he do it? He added bends and trills and exquisite timing eliciting deep expression from every note, maximizing the potential of each without wasting energy zipping up and down the neck like a shred-wizard. Zipping up and down creates opportunity for error, activating a lot of genes to do the work of life creates room for mutation and most likely - error. Our genetic machinery has developed a system of modifications to DNA and genetic material that leave the genome relatively uninterrupted.
JBT - Nature loves stochastics. The crap shoot. The tossing of genetic spaghetti against the wall. Some will stick and become 3-D wallpaper with mold growing on it and crud collecting in the groove where round spaghetti sticks tangent to the flat wall. This groove will be difficult to clean and elbow grease expended in cleaning may cause spaghetti to drop to the floor. Every target has its bullseye. We shoot our 20 arrows and none hits the bullseye but the target is full of holes. We have achieved our intention.
We are what our grandparents and parents ate as well as what we eat. See: “Dutch Hunger Winter” http://www.naturalhistorymag.com/features/142195/beyond-dna-epigenetics
We have our genome, a hardworking epigenome and a proteome. Think of the genome as a library with 20,000 1-2 billion year old books ( treasures for certain) Each organ system cell group carries the entire library within its membrane. Each cell type checks out its book during a life and reads its own story. The check out and reading portion of this story is called epigenetics. Each of our cells can activate its small region of this vast library and keep all other “books” locked up tighter than a drum head - inaccessible, not in play, every book in every cell. At the liver there are 111 genes for liver function switched on in 175 billion liver cells and few others - most others remain inaccessible no need for neurons or heart muscle, bone or epithelial cells at the liver. Think of a war game: Each of the four branches of the military gets the entire battle plan notebook. The Air force version has a tight band around the Army Navy and Marines pages.
Definitions:
- Kodalith: A photographic film that turns a photographic image into black or white - no shades of gray. Zero subtlety, the world is either black or white with Kodalith. The tone-scale of a human face or a landscape has a thousand shades of gray, from just above black to just below white. Kodalith film will turn every tone less than 50% gray into white and every tone more than 50% gray into black, creating an image that is boldly black and white. Think of this as a switch: on / black and off / white.
- Epigenetics: Inheritance that cannot be explained by genetics.
- Epigenetics ( more recent) Molecular change but not to base pair sequence.
- Epigenetic processes dominate cell function. If a human/mammal body is the Roman empire, the genome gives a general his marching orders from Rome and all other actions of the army all the way up into northern Britain are defined, described and carried out via the epigenome using PTM.These are modifications to DNA, RNA and histones that are exposed for further action by the loosening of the tightly wound chromosome. This now active, unwound stretch of DNA is a very small percentage of the total DNA present in a given cell.
- Epigenetics: The greek prefix “epi” means “upon” upon genetics. An epigenetic event changes the expression of a gene WITHOUT changing the DNA i.e. without changing the sequence of nucleotides. Using Nessa Carey’s analogy, imagine checking out a library book for three days. This book is a part of our total DNA, the library. The book is a gene. While we use this book we place post-it notes on several pages to clarify the meaning of certain passages, to add the detail of our thought. When we return the book we have removed the post-it notes and the gene and the total genome remain unchanged. No DNA has been changed, no base pairs have been added, subtracted, edited or changed in any way. My epigenetic work was upon the gene but did not change the gene. If the gene is changed it is NOT epigenetics, it is a gene mutation.
Epigenetics, though becoming a popular field of research in bioscience only 20 years ago is known to be THE process that differentiates one cell from another during pregnancy. A zygote, the fertilized egg, has 46 chromosomes with their 6 billion base pairs the moment the sperm penetrates the egg. A fertilized egg is a single cell and before the cell divides for the first time, this cell can become Any cell in the body among hundreds of basic types. All cell differentiation that follows is epigenetic.
This set of library books begins to get post-it notes assigning organ function and metabolic tasks soon after fertilization, as the cells in a fetus begin to differentiate. As cells in the fetus differentiate the entire library carrying the code for the entire body and everything in it, is present in every one of what will become 37 trillion cells. The tasks characteristic of each cell type: heart, lung, brain, skin, blood will be activated by PTM.
A cell becomes unique as soon as it checks its book from its cell library that contains 20,000 books. To check out a book i.e. to begin the process of cell differentiation is itself an epigenetic action. Think of checking out a book as placing a post it note on the cover of the book thus acknowledging that it is a brain book and not a liver or heart book The liver cells check out the liver book and leave the other books undisturbed. The brain cells check out the brain book and leave all other books on the shelf alone. Remaining on the shelf means that the DNA remains tightly wound up and thus inaccessible to the specialized tasks surrounding it and that have been activated by the checked out / activated / enabled / switched on kidney book. During pregnancy the books begin to get read and collect the notes that further describe their function. Many post-it notes are applied as organs begin to do their specific jobs in the growing fetus.
The cells of the fetus check out their unique book depending on assigned organ system during fetal development at a specific moment. The body plan book is checked out early so the baby’s head is at one end and the budding feet at the other end and then arms and legs appear as buds in the proper geometric alignment i.e. bilaterally symmetrical not radially symmetrical. There is a head librarian book checked out early that orchestrates the development of the entire organ system. Though the brain book gets checked out early in fetal development, all primary post-it notes are in place at birth but Post-its continue to be stuck to brain cell pages until death as sensations are sensed and memories are formed and retrieved. Many neocortical functions may undergo structural differentiation through childhood.
All cells have many structures and metabolic functions that are identical. All cells, no matter what organ, must process energy and expel waste and, unless a neuron, reproduce itself. The genes that control these foundation functions are active in every cell with minor exceptions. For this library analogy it is assumed that the books ( genes) carrying out common cell functions are in play from the beginning and are not epigenetic simply normal gene-protein synthesis cycles.
- Transgenerational Inheritance: Lamarckian inheritance of acquired characteristics.
JBT - Our brains can take a field of black and white dots and transform them into 1,000 shades of gray. The tiny dots that make up the fully-toned black and white halftone images in a newspaper are either black tiny dots or white newsprint - no gray involved in this printing process but we perceive many of the rich tones of the real world present in a normal black and white photo. The sensory effect of kodalithing is transformed as the scale of the field of action changes.
JBT - Kodalithic - black or white, present or absent, on or off. The core idea for the computer age, digital technology is binary, biology is also binary. binary-ness is at the core of all living things. The halftone newsprint image comprising black dot or not to obtain the elaborate gradation of a black and white newspaper photograph is analogous to cellular biological process. PTM adds the entire gray scale to the foundational information delivered by the expressed gene. This gene, as it is switched on or off, launches a cascade of action that lasts until the cell dies; 13 days for white blood cells, 30 days for top layer of skin cells, 120 days for red blood cells, 18 months for liver cells and a lifetime for neurons.
The gene that differentiates a pluripotent cell into two types of cochlear nerve cell is switched into its cochlear-ness at ten weeks during pregnancy. In a 2-step process of cellular events there is the primary epigenetic event that commands activation of cochlear cells and silence from other sensory cell types ( we don’t smell with our ears or taste with our eyes). Once the cochlear nerve cells have become black dots in our halftone image, we no longer have a cell blank slate with pluri-potential. These cells are now dedicated to the audio club for as long as they live.
You have seen the big photo collages that take 10,000 pre-existing photographs and arrange them all as if each were a tiny splash of color. There are two levels of picture-making at work here, one for the first, smaller image and the second where the small pic is put to use as only a patch in the large image. Think of an organ’s cells like one of these larger images. Step one is to make a picture - a cell differentiated for a specific organ step two is to assemble an array of these each with its own special character into a big picture - the audio picture or the liver, kidney, lung, brain picture. The big picture is that we can listen to Beethoven and look out across the Grand Canyon and taste a fine meal as we cough, sneeze and sweat at the right time.
JBT - Effective communicators simplify ideas for better comprehension losing detail in the process. This abstraction for communication is Kodalithing. If Kodalithing is at a small scale it is barely seen as such, George Washington has a memo drafted by his aide Alexander Hamilton and sends it to Congress as his own. The historian says this memo was from George Washington to Congress, Alexander Hamilton is lost in the Kodalith. If all events involved in a history of the American Revolutionary War were told at the level of the Washington-Hamilton memo source, the history book would be 15,000 pages instead of 500. To omit mention of French participation in the American victory over the British would be excessive Kodalithing, too much meaning is lost but we don’t say the American-French forces defeated the British. We say the Americans defeated the British.
JBQ - Did methylation replace mutation as the key driver of a finer-tuned Natural Selection in the Darwinian model? Say about 150 million years ago? Genetic mutation was key when the fundamental chemical-structural operating system was being born from 4.5 BYA to 150 MYA then PTM took over as a finer, more flexible system of evolving. Errors were not so irreversible with methylation. John Trumbull begins his large painting with a mop ( DNA sequence) and finishes it with a fine brush: methylation, acetylation etc. Perhaps there is a hierarchy of finality beginning with the nucleotide sequence itself then to the methylation etc of the nucleotides at the gene site, then down the ladder to histone modifications, all of which can be heritable as cells replicate during one’s life and across generations. may look junky but all of this ADNA is storing the actors in the histone story in order to survive meiosis-mitosis. A gene mutation is a VERY big deal and at this juncture in evolution almost always a bad idea but gene methylations and histone mods are just fine and more easily corrected or erased. Cosmos to organisms “Don’t mess with a good thing, we’ve made it this far, do not screw this up. Leave DNA alone. Use PTM to secure change.
JBT - Once a Kodalithed image is encoded into our neurons it is difficult to change. For example let’s look at “Waddington’s Hill”, an heuristic developed in the 1970s by Professor C.L.Waddington to describe epigenetic cell development. The geography of this hill is such that as a ball rolls down there is a dividing hillock where the ball will roll either left or right. Once it has rolled to the left or right at the first juncture, a major causal path is established, as the ball rolls further down there is another outcropping that presents another left or right option and so forth until the ball is at the bottom of the hill in stasis. The ball will want to remain in stasis. It will require energy to move the ball, either back to the top of the hill or to an adjacent valley. Think of the descent from the top as the transition to greater complexity in a cochlear hair cell. An empty brick warehouse will make a fine office space. As we begin, there is one vast empty volume. All space is undifferentiated. We are at the top of Waddington’s hill. As this undifferentiated space becomes offices, conference rooms, kitchenette, toilets we approach the bottom of the hill. Walls have been built, lights installed, plumbing is in place. Here at the bottom of W-Hill it is costly to change the interior architecture.
JBT & N - The opposite of Kodalithing is TMG ( Too Much Gray). To be TMGd is to be buried in detail, in so many shades of gray that the truth that may reside at either pole of an argument becomes fogged. As Stephen Jay Gould knocks Charles Darwin from his pedestal, a Kodalith moment, he disguises the paradigmatic violence in 1,000 shades of meaning with his jargon,history lessons, apologies, false encomiums, goofy science, impenetrably sloppy diagrams, straw-man attacks, squid rasslin and much else. Its all good, a great stimulant for thought.
JBT - There is much Kodalithing at work when credit for a great discovery is assigned. Newton-Leibniz, Picasso-Braque, Ellington Strayhorn, Jones-Jagger, Lennon-Parker. The individual with the best historical PR team wins the credit sweepstakes. “Satin Doll” everyone knows it as a Duke Ellington not as a Billy Strayhorn song even though Billy wrote it. History loves Kodalith as do historians. Shades of gray nowadays mean shades of dividing up profits.
JBT - The human brain Kodaliths for many reasons. It is the only way to store a memory. The histones surrounding the DNA in a neuron are either methylated ( black) or not (white). these neurons can accrue into patches containing many thousands for a single vivid memory that includes sight, sound, vome, taste and touch i.e. the dotscreen at a newspaper image ( each momentary sensation is its own dot and they arrive in groups from different senses) but it is still kodalithing. As the total number of memories cascade into larger realms kodalithing must occur in order to make room i.e. those 100,000 sensations from a great first date get kodalithed as all ON-Black and filed as a single great memory in a bank of 100 date memories. It may be parsed out-remembered in detail, later at will.
JBT - Kodalithing concentrates meaning into essence ( see: Kara Walker cutouts: http://en.wikipedia.org/wiki/Kara_Walker
Sometimes essential meaning is lost during this process. It would be difficult to contain the meaning of a watercolor painting with kodalith film as it is the fluid-induced shades of tone that are the essence of this medium.
JBT - Structuralism asserts that our brains arrive on Earth containing a waffle iron, a neural appliance with six structural grammars enabling more than screams, grunts, chirps, scowls, howls and arm-waving though all of these are still very much in use. Imagine that our built-in, ADNA coded waffle iron contains six different grammars, one each for spoken-written language, music, smell, touch, taste, graphics and architectural space and that our neocortex gives us the brain volume to add coded cultural specifics to each of these structural capabilities for communication. Sensation is processed by each of six different brain areas of sequential evolutionary age from oldest to newest: brainstem, amygdala, hypothalamus, thalamus hippocampus, neocortex.
Each of these six brain areas has its unique method of judging sensory information, its own version of a waffle iron. We have the viscero-emotional grammar of our limbic system expressed along the Papez circuit, emotional grammar, logical ( written/spoken) grammar. We have a grammar of pleasure and one of pain, one of smell and taste. We are born knowing the decayed-dangerous-don’t eat from the sweet-fruity or fatty-bloody edible.
JBT - That lines are ever points is a fluke of human perception. That continua may be parsed into singular events is a myth, a misperception always leading to error. We make this error as a matter of course. There are no points. Points are kodalithic phenomena, the mind’s effort to create meaning via abstraction. Beware of all that is lost when time or space are stopped. Nothing ever stops. Nothing is ever still. There are no points in time or space. Our mind creates points in time and space for convenience, to get a handle on living. We call these points memories, each memory has a unique combination of sensory information.
JBT - Our idea of a house, what a house is, the very nature of any house is a point in our memory, a fixed idea locked into our brain at an early age. All memories are fixed and revisited only when necessary - as Eldredge and Gould pointed out, stasis reigns until evolution is required. Our ideas about the nature of art and science are as fixed as those of houseness. “Science is rational requiring experiment and proof” “Art happens on a canvas and is displayed in a museum or gallery.” After we buy these notions close to the symbolic foundation, we can add detail. Human consciousness is a collection of paradigms for 1,000 things; art language, dance, all systems for processing sensation and storing memory.
JBT - A memory is a dot screen, a patch of tissue with 1,200 available loci each of which has been turned on or left off i.e. kodalithed. 200 dots each register sight, sound, smell, vome, taste, touch and each sensation has an intensity tag. Imagine a six section waffle with each section formed in its own area of the brain followed by stacking into a single more abstract, more compact package for storage. When you remember Paris now and then you won't remember 200,000 sensations you will remember “nice”
JBT &N - DeAcetylating seven histones at a gene in 1,000 neurons storing a hurtful memory is DA Therapy(DAT) . DAT is 50% couch analysis and 50% lab work-chemical adjustment, detaching PTM that codes for intensity as we change the memory of a violent beating from father into a love tap, freeing the mind to accrue self esteem. The PTM we removed is evacuated from the neuron as cell waste where this dark memory maker will be flushed by the kidneys and pissed into oblivion.
JBQ - Is there a structural difference between a heritable acquired characteristic TTT (Transgenerational Transmission Trauma) and a run- of- the- mill very bad memory during a life? if the TTT is locked via PTM then there must be a location in a neuron for this and that is visible at least in theory. Some tangible molecular thing must lock into the genetic material in the germ cell in order for inheritance to occur. Is there a threshold where a very bad memory gets transported to the germ cells by some increased voltage from the brain through the spinal cord to the uterus or testes?
JBQ - Are not all epigenetic post translational modifications at germ cells heritable?
JBT - All bees are born identical and differentiation into queen or worker happens as a result of diet. All begin their lives eating royal jelly, the workers are weaned from it to a diet of sucrose after a short while. The queen continues to eat royal jelly her entire life thus remaining a queen throughout. Perhaps human military leaders are selected in a similar manner with normal men separated in every physical way from their mothers by age 18 whereas a future military leader’s mother will follow him to West Point and iron his shirts and succor him during stressful periods -see:Supreme Commander Southwest Pacific Douglas MacArthur. A disproportionate number of corporate, military and political leaders had close physical attachments to their mothers.
JBT - Perhaps trauma such as that experienced by concentration camp survivors during World War II interferes with PTM scrubbing as the zygote becomes daughter cells resulting in trauma that has been stored in ova at brain genes( perhaps as ubiquitinated histone #3) to remain at this chromosomal location during fertilization and fetal development in the nervous system and growing brain as this memory is transmitted to children.
JBT - Sustained neuronal voltage spiking during the formation of long-term trauma causes DNA to unwind from a nucleosome at several neurons creating neuronal chromatin available for modification that would otherwise be tightly wound around histones and thus inaccessible. Perhaps the voltage spike allows histone modification to occur in a tightly wound gene through brute force with no unwinding required or the DNA itself simply gets coated with the modifications with no histones involved.
JBT -Epigenetic activity is spread from its initial neuronal site via very small RNA delivering epigenetic response from one location to distant parts of the organism, to the germ cells perhaps, where epigenetic change is inherited. “Plants use epigenetic modification to regulate 1,000s of genes helping to maintain appropriate but “short term” response to the environment” N. Carey
What is “short term” one single moment in time, say a single season or a single organism lifetime or short term as in the life of the species rather than the life of the entire clade, say 5 million years instead of 250 million years. Epigenetic activity as a way to cycle gene expression during a single lifetime on-off i.e. one cycle per lifetime.
JBT - RE: effects of protein folding on phenotypic expression. To do: get 200 copies of “Mad” magazine with the folding back cover that, when folded, creates two distinct pictures. See what percent of pictorial space became shallower and percentage of deeper pictorial space i.e. does it become a close-up or a further away image?
JBT - All new brass keys of a certain brand produce blanks of a general configuration. Each of 100,000 blanks has exactly the same relative percentages of copper, zinc, mercury etc. They are all the same shape and weight and chemical composition but minor variations in shape at only one edge create 100,000 different key identities for 100,000 different locks. If this holds at such a gross level then surely it works at the cellular-molecular level with DNA, histones,RNA of all sorts and proteins.
JBE - Examine experiment results noting the presence of a molecule and its time of arrival or departure tells us something but not nearly the whole story. It is the actual 3-D shape of each molecular variation that begins to tell the story. Look to histone shape for info re: memory not simply the fact of PTM. OK, histone H2B is citrullinated and a neuronal gene involved in memory is suppressed. This is like picking up Moby Dick and noticing that it is about a whale. Look to molecular shape for additional story. SHAPE AND MEMORY. A traumatic memory has a unique shape as does a blissful memory. These shapes combine and affect one another creating an overall color to the memory is it bright springtime pastels or is it mud and gravy with 90 years of grime.
JBT - Perhaps we have a system that reads electromagnetic radiation from a specific shape of molecule giving added information - another, deeper level of on-off switches, another level of dot pattern, another layer of Kodalith and after shape is detected and categorized we move to the next adjacent deeper level, orientation to magnetic north or body north or some reference point say at the center of the thalamus there is a ground zero a GPS marker, a USGS benchmark, a reference point. Our own Greenwich Observatory - home base for all global ( brain-case ) neuronal navigation. every molecule involved in neuronal memory storage sits in a specific 3-D relation to this quantum point in the center of our brain and position becomes information. Thus a single cut key ( ubiquitinated histone 2A) can have its own 1,000 positions - variations storing much memory. So a bash to the head erases memory, jiggles a brain full of specifically oriented molecules. Some jiggle back into place and others do not, amnesia ensues.
“Waddington’s Hill” A sloping conceptual landscape with an array of channels one nearest the top splitting the field into two follwed downhill by two splitting into three possible options, decision points in time for a growing thing. These channels guide a ball rolled from the top into either one of two, this happens twice resulting in four possible end locations at the bottom of the hill.
“Blake’s River” begins as a beautiful mountain stream near its source where one can easily step across, it gradually becomes a mile wide muddy river filled with crocodiles that is difficult and dangerous to cross. This could be one’s river of education think how simple it is to go to college along with 90% of the college population and how difficult to matriculate as a mid-career working person. Evolution of an organism follows Waddington's HiIl ( he called it a “landscape” hill is not only a shorter word it has the grade change built in) as complexity increases options narrow and it becomes difficult to roll back uphill. As in Blake’s river it also becomes dangerous. the deep history of an organism has a lot of genetic mutation as it evolved from simple to terminally complex but at present 99% of genetic mutation spells malformation and disease. Due to the imperative that genes are to be conserved, our DNA has evolved epigenetic process allowing phenotypic difference in cell expression without changing the DNA. Blake’s River, like the Mississippi, Amazon, Danube or NIle has eddies, swamps, backwaters, hidden sandbars and snags i.e. it will often fool you, it is not always what it seems, it has force and power and inevitability and risks obscured by its easy nature.
JBT - What if one’s neuron PTM pattern got re-distributed along the brain DNA and neurons began to pulse like heart muscle cells, your brain now pumping out great ideas?
JBT&N - If a memory is locked in at a neuron group as methylated neuronal DNA or neuronal histone mod at hippocampus, it then has 60 years (plus or minus) to sit there and do any number of things such as sending information via methylated miRNA down to an egg via axon microtubules at spinal cord and out to ovaries thus locking this memory into a germ cell neuron nucleosome as a DGM ( Deep Genetic Memory-jb neolog)
JBT&N - 99% of conscious experiential memory is epigenetic and stored in brain neurons. The memory required of cells to distinguish their purpose at specific organ or tissue or hormone is epigenetic ocurring just after conception and removed from the genome with each generation to begin again as totipotent zygote. The species uses DNA as memory storage system. It is rarely interrupted and usually by detrimental mutation. Traumatic memory appears to have a pathway to permanent storage as heritable. To do: check for N. Kellerman’s TTT in mouse population. Specifically, check DNA / histone PTM patterns at mouse hippocampus-ovary-germ cell axis, the HOA axis, a JB neologism.
JBT - If we have neurons outboard of the brain at heart, lungs, gut perhaps these neurons are relay stations for memory shipping from hippocampus to testes and ovaries.
JBT - We may inherit the fears of the past few generations as a matter of course, no need to wait for browbeating from parents, siblings, teachers and media. We don’t need a slap in the head to be afraid of being the “tall poppy” or a follower rather than a leader due to pre-wiring so when on the analyst’s couch we shouldn’t restrict blame to parents but must include gramps and granny though deceased, still bearing the psychic burden that has interrupted our rise to social significance and spiritual enlightenment.
Fun Fact-1: Two highly specialized cells, egg and sperm merge to create a totally un-specialized cell capable of becoming any one of 200 different primary cell types in the human body and each of these 200 has many subtypes. there are more than 70 types of neurons. Most epigenetic memory gets wiped from the genome just after fertilization. A quick wipe for sperm, a slower wipe for the egg.
Fun Fact- 2: 42% of human genome comprises transposons probably viral residue. 1AP retrotransposons do not get erased during meiosis-mitosis-zygote-fetal development. Perhaps retrotransposons are the site of Transgenerational Transmission of Traumatic memory.
JBQ - What if 30-40% of human DNA is virus, bacteria, fungi or mold and is currently shut down by PTM? Humans as seed banks for microorganisms.
JBT - Cezanne had great admiration for Chardin and tried to capture Chardin’s magic in his later work. It was Cezanne’s failure at Chardin that created his great victory for a new painting - Cubism
JBT - Investigate the reading of color of a molecule by a second molecule for operational cues, its electromagnetic signature, the electromagnetic wavelengths it reflects or absorbs as signals for further metabolic or structural activity.
JBT- At neurons involved in memory storage look for lots of unspooled DNA at chromatin as it prepares to receive and encode memory.
JBQ - What is the viscosity of mature chromatin at a 55 year old neuron? Does mature adult chromatin at hippocampal neurons get less viscous as memories fill up space at histones and ADNA as memories lock into place? We know that we die with the neurons we are born with i.e. neurons are not replaced as are skin or liver cells. does this mean that the chromatin in neurons never gets replaced, renewed, recycled or in some way refreshed? Does a 70 year old person have 70 year old chromatin? might this old substance be getting sour or debased / infected in some way as it is invaded by bacteria, virus, archaea, fungi or mold even if not subject to Alzheimer’s effects i.e. there may be a spectrum of ways to interfere with normal youthful neuron function.
JBE - Does neuron chromatin get more firm with age as memories lock up chromatin? Is viscosity of neuronal chromatin affected by a rat’s accrued experience running mazes and learning tricks? Does a highly trained rat with a brain full of maze memories have more firm neuronal chromatin than a tyro rat?
JBQ - What is the correlation between ADNA and the Structuralist phenomena asserted by Saussure( signmaking) Levi-Strauss(classifying plants and animals) Barthes(myth making), Chomsky ( grammar) i.e. the stuff of our humanness?
JBQ&N - How is an emotion memorized? How many steps in the cascade of on-off switches at work while storing sadness or happiness? Must there be visuals? If five senses are involved, are five brain areas alerted when this memory is recalled or have the sensations been packaged as gestalt and stored as a unit - a MU - memory unit. A memory unit is a single retrievable thought comprising ten thousand separate inputs from all sensory systems as well as neocortical judgement / analysis tags that have decreed this experience rich, full, complex, worth remembering. Are songs or paintings symbolic storage devices relieving our brains of having to store all aspects of a certain sadness by giving an appropriate song that perfectly captures the zeit. Edith Piaf packaged a lot of emotion in her day.
JBQ - Does a cluster of neurons storing a particular memory get an intensity tag scaled from one to one hundred? Has our brain ranked every person we know in a hierarchy of importance so that there are two tags with every emotion one for intensity and one for importance of person involved? Is there a primordial circuit in the brainstem that combines importance of person ( who, in this example, is a nobody) with the overall intensity of an incident? I experience a huge beer-spilling intentional bump in a crowded bar causing a pulse straight to my amygdala-motor axis signaling: “Mama said knock you out”?
JBT&N - Quantum Memory Transfer (QMT) - A memory comprising 100,000 sensations over a hard year resides in the brain as a neuronal bundle of ADNA stored at a small part of a specific voxel ( one cubic millimeter) in the hippocampus as a long-term memory. This potent bundle can be sensed-read-felt-known by another person in some detail. Perhaps a child is not born with a holocaust induced traumatic memory from parent but the child is hardwired by its inherited ADNA to receive this traumatic memory. This child is born with a PTM histone that does not contain this entire evil memory but only half of the abstraction of it, like half of a DNA molecule. A child of traumatized parent, grandparent or great grandparent will add the complimentary half of this ADNA-Histone thus recreating the whole memory just as the ribosome constructs a protein from a stretch of mRNA. The child, after reconstituting this traumatic memory has been Kodalithed. An experience that played out over two years in a concentration camp with billions of sensations stored by the experiencer as a million PTM neurons and inherited as a single bundle of PTM histone in a germ cell ( ovum) where it became a incipient brain cell in the fetus and grew into a mature neuron cluster ready for activation.
JBN - A memory bundle ( MB) - The kodalithic abstraction, the sign, the stored experience, the switch is on, the myth emerges from stored experience generated by six senses and many neocortical judgments. The sixth sense being vome, short for vomeral-nasal our pheromone response: “chemistry” as opposed to “The Smell Test”.
JBT - Epigenetics is to genetics as post-Hubble astronomy is to looking at the moon through binoculars. Our genetic code with its 3 billion base pairs is only the starting point. This fact, like the universe itself, is overwhelming. Humans continue to underestimate the complexity of life. Imagine the human brain as big as Rhode Island, now let’s take a drive to the hippocampus and watch a memory unfold.
JBT - “A Taxonomy of Culture” All human cultures have created a tissue of myth in order to defuse a gnawing insignificance. The micro-totemic quality of many of our current mythical referents has become flexible. Studying The Beatles or Bob Dylan at a university, not to mention our obsession with entry level celebrities. there is a taxonomy of cultural concern but in the big picture it is all the same stuff whether Beyonce’ or Catherine The Great, Winston Churchill or Chubby Checker, Goethe or Seinfeld. One gets more credit for name-checking an Ancient Greek than a 1950s rock and roll star but they are not essentially different. The former is swathed in time. One day Beyonce’ and her retinue will be studied in universities and revered as if Cleopatra.
JBQ - Phosphenes are the brilliant, psychedelic color patterns you see when you press on your eyeballs while lying in bed at night. How are humans able to see the explosive array of brilliant light and color of phosphenes in total darkness, no light whatsoever, no electromagnetic sensation, no photons striking the retina?. Are phosphenes a chemical light only? Pressure on the eyeball releases calcium or potassium ions activating neurons? Do these sensations find their way back to the occipital lobe for neocortical processing or does this sensation stop at the brainstem? We don’t really need a neocortical opinion about the meaning of it all. Do phosphenes involve memories of color stored in the brain?
JBT - Every atom in our universe is connected to an alternate universe via a nano black hole in its innermost center at the sub boson-quark level. This subatomic connection to our next adjacent but unseen universe is the source of gravity.
JBT - Human culture vaccinates us from the affliction of our insignificance, giving us a scale of being, a starting point with which to face the universe. Our neocortex is a mechanism enabling us to play off against one another in an invented, wholly arbitrary and myth-riddled social engine, a coded system of symbol whose turbulent convection creates intra and inter-tribal social stratification. Conflict of one sort or another is the lubricant for all cultural motion from relationships between nations and lovers.
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May 17, 2015 6:35pm