Archive for September, 2015

Albedo Logic


“The solar magnetic field has long been known to cause the sunspot cycle. The physical shape and activity in the corona also varies with the sunspot cycle. The solar magnetic field is known to be able to transfer large amounts of energy to the solar atmosphere. It is possible that the solar magnetic field is the ultimate source of physical heating of the corona.” -NASA website

The sun’s surface is 6,000 degrees celsius. The sun’s corona is one to two million degrees Kelvin.  Note the two temperature measuring systems.

Albedo: Reflection coefficient – the reflecting power of a surface. The ratio of reflected solar radiation from the surface of the Earth to incident radiation upon it. Albedo is expressed as a percentage and is measured on a scale from zero for no reflection ( charcoal) to one for perfect reflection of a white surface – fresh snow is close to one on the scale.

The albedo effect is the tendency of highly reflective,  ice covered Earth to cool as it reflects sunlight and conversely, the tendency of less bright, more absorptive landforms and plants to absorb light/heat and to warm up. The cool get cooler, the warm get warmer. Note economic albedo effect as rich get richer and the poor get poorer. Warming and cooling economic and subsequent physical effects of “warming” and “cooling” on residential and commercial neighborhoods.

Precession: Axial and Apsidal:  The wobble of the Earth’s axis is axial precession, the Earth wobbles through 360 degrees every 25,000 years. Axial precession affects the Earth’s weather.  The rotation of the Earth’s elliptical orbit around the sun is apsidal precession, this also affects the earth’s weather.

Do sun cycles of heating-cooling caused by its magnetism or other mechanism affect Earth’s climate?

The Earth has experienced five major ice ages in the past 3 billion years. During three of these ice ages: the Huronian, Sturtian and Karoo, the entire Earth was a giant snowball. This ice-snow was up to five miles thick. The volcanoes and hot vents in the Earth’s surface did not cease to exist when covered in ice, they created large and small lakes, pools, ponds, rivers and streams teeming with microorganisms in the total darkness. There were places where columns of heated water penetrated the surface of the deep ice where life was exposed to sunlight and the atmosphere. There were convection currents in these extremely tall water columns as warm water rose and chilled water descended. This turbulence allowed much intermixing of organisms and some synthesis of molecules large and small and biosynthesis of entire single-cell organisms: bacteria, viruses, archaea, molds, algae, and much larger single-cell organisms the protists: amoebas. A great merging of DNA, RNA.

Many amino acids required for life were present in subterranean pools during the Huron ice age. Proto-RNA molecules evolved a code for each of these so that a protein could be assembled at a cell rather than assembled willy nilly from the soup.

An organism has a system for creating RNA code for an organic molecule it encounters and a capacity to store this info at its RNA. RNA  reverse engineers a code from free-floating molecules and assigns a code to recreate a desired molecule.

How does non-coding RNA install the code representing a new protein into its string of nucleotides? The code is cut from a visiting microorganism and pasted onto the RNA of the host.

Pocked Snowball – Imagine a spherical chocolate chip cookie made with very small chips. This would be the surface of snowball earth with the chips being geothermal puddles, ponds and lakes, all separated from one another and each containing its own variation for the recipe of life. Thousands of distinct microenvironments. The ice melts in a band around the equator linking 1,000 of these separate petri dishes. There is a microbial barn dance, a carnival of symbiosis, when mixing and matching and shacking up result – biosynthesis. more complex organism evolve from the simpler models of the pre-glaciation epoch.  The glaciation forces dense concentrations of a wide variety of microorganisms into one another as their ecosystems shrink during the approach of the big freeze. They thaw in this state of togetherness in a very crowded environment during the snowball melt. As ice recedes, their territories expand.

Imagine 100,000 separate pools around the globe resulting from meteorites bearing amino acids, pools created at thermal vents, pools surrounding volcanoes. Every volcano has its surrounding lake on or below the surface of iceball Earth. The lakes do not merge all at once. first two then three then 1,000 or 1,000,000 years later a fourth pool is added then  10,000,000 years later, a fifth. Pools and lakes merge four by four during next 10 million years until there is an ocean.  Lots of time for small groups to get to know one another before merging into a more varied assembly. Earth was not one big interconnected primordial soup during glaciations, it was 100,000 different organic assemblies for life. As the ice melts, as Earth’s atmospheric chemistry changes, still more cause for evolution. There were myriad different micro-environments for 10 times myriad recipes for primordial soup. Each volcano erupts through a unique geological core chemistry to seed its isolated lake with the chemicals of life.

Imagine a geothermal pocket, a “Hot Pocket” or call it a “Steam Dome”  four miles below Earth’s ice surface, a pocket half filled, say 1,000 feet deep, with water and a void between the inside surface of the ice dome and the surface of the subiceerranean lake the ice dome filled with a warm, humid atmosphere. Each one of the countless steam domes has its unique chemical-atmospheric environment, Each hot pocket and its magma pocket, linked by cracks in the Earth’s crust is like a glass tube in a lab with two bulbs, one at each end – one molten rock the other warm gas hovering over melted ice. A test tube for life. Imagine the large array of micro-environments in such a steam dome and the fluid temperature gradient from the hot vent to the cooler fluid of the edges. The drippy underside of the dome – stalactites of concentrated chemicals, new surfaces for life. Pressure builds up within the vast dome and cracks find their way to the ice surface as they zigzag up through three miles of the stratified ice cover to the surface and sunlight.

One deep dome creates 50 small lakes at the surface. The dome expands to vast proportion and then it breaks the surface allowing sunlight every day and whatever atmospheric cocktail is at hand to influence the microorganisms. Imagine the Pantheon in Rome with an ice/ice water floor and a dome of ice and the oculus. The hole in the dome expands. In 500 years a very large lake has formed. Many of these large lakes, former domes, merge at the equator as the Earth emerges from its ice age due to reverse albedo – a warming due to larger and larger expanses of sunlight absorptive plant life and exposed rock. A band of blue water encircles snowball Earth. This equatorial band of water has two shorelines that encircle the Earth a north shoreline  and a south shoreline, a widening band teeming with microscopic life in between.

The ring of blue water expands and twists and turns as new continents are revealed. The very thick ice is thinning always changing the chemistry of its pools. New comets and meteors strike and new chemicals of life are delivered from space. Imagine an under-ice lake 500 miles wide with an oculus five miles wide with the solar heated patch of water on the lake surface. What sort of ecosystems would evolve from such a structure with its geothermal vent issuing hot water 10,000 feet below? It would have warm humid air at the center and cool humid air above  the 1,570 mile perimeter, clouds and rain below the ice dome.

A volcano would create an entirely different 500 mile diameter lake on the ice Earth surface with its volcano at the center and unique weather circulating around the active cone. A volcanic ice bowl. Perhaps much warmer water in this lake with sloping walls up to the rim of the ice. The Earth would have 1,000s of these volcanic lakes in the ice – another type of pock.

Foundational diversity from the following:

  1. Desperate marriages-symbioses as organisms try to stay warm, conserve energy as the Earth cools, ecosystems shrink and great ice sheets spread.
  2. As ice spreads microorganisms become more concentrated in smaller unfrozen environments. They cannot avoid one another and soon they are crawling all over one another, smooshed against and forced into one another as ice grows. 
  3. Microorganism enter dormant deep freeze state while merged during Huronian glaciation -compressed genomes are not united at this point –  just trying to stay warm and failing. After sharing the same lipid membrane, frozen in the ice for five million years as one, they thaw and believe ( chemically) that they were always one thing and proceed through evolution as such. Not only mitochondria entering and aiding protists but 1,000 organisms entering 100,000 others – myriad combinations – mixing and matching toward the big freeze and while emerging from the big thaw millions of years later or evolving continuously if near a warm spot.  Is there a metabolic cycle affected by a freeze-thaw cycle that accelerates symbiosis?

Scenario One:  Chicxulub-scale meteorite striking the three mile deep ice of the Huronian glaciation. It would send a cloud of ice around the entire globe causing a great acceleration of the cooling albedo. A deep dive into iciness. Ice dust in orbit for many years and ice dust storms all over the surface of the Earth. Albedo out of control getting colder. Visualize rings of ice orbiting the Earth like the rings of Saturn.

Scenario Two:  All life on Earth began in Yellowstone Park near a large cluster of vents that prevented total ice coverage. The park was surrounded by a slope of ice that stretched at forty-five degrees for 4.24 miles to the ice crust rim. A comet impact at the thick soup of Yellowstone microorganisms spread bits of life  along with ice particles to all parts of the globe. Raining life onto ice water pocks the world over where countless emergent genomes diverged from those of Yellowstone. Life gets a one billion year head start at Yellowstone before spreading around the world,  seeds planted in the ice.



Economic albedo effect: Growing poverty / disarray begets poverty and disarray until hell freezes over – must have volcanic input into moribund system to reverse economic cooling.

See: Multi-strand woven steel wire cable as metaphor for rhizomic culture. Note cable cross-section of concentric bundled, varying diameter steel strands. One of the world’s great engineering developments: Albert, Smith, Newall, Roebling,Hallidie, Stone et al. Envision core cultural “givens” strands of language, religion, plant-animal classification, marriage-kinship, definitions of mental illness and crime, ethics, etc.

Liberal theory and politics and policy has, as its core notion, the dissolution of the  family. No father – black or white, rich or poor – dad is marginalized or gone. In anthropological terms, liberalism is a product of the matrilineal mind.

A thought inspired by Foucault @ “Madness and civilization” Children as gradient reducing elements between lonely parents  and the cosmic void; to be nurtured like the surface of the Earth nurtures plants, animals and microorganisms in order to span the differential between the hot sun and cold, dark nothing much, reducing the gradient.

At one bioscience website 3 billion is written as the approximate number of nucleotides ( single bases) at another bioscience website it is 3 billion base pairs. One of you is off by 3 billion. Can we come together on this?


September 27, 2015  5:07  pm



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Kodalithic Kodalogic


Kodalith is photographic film (obsolete) once used by printing companies and commercial photographers. Kodalith film reduced 10,000 gradations of tone, perceivable in nature by the human eye, to black or white only, all gray is washed out to either end of the scale. If a surface reflected less than 50% gray this film recorded it as pure white. If the surface reflected more than 50% gray, it became black. When developed, the photos taken by this film had no gray whatsoever,  just bold black and white.  Something is kodalithic if its complexities have been reduced to black and white.

Black and white are qualities of the visual world but all sensory, intellectual-philosophical phenomena can be reduced to polar terms.  The matter at hand is either black or white, conservative or liberal, hawk or dove, scientist or artist. Music is either tonal or atonal, food tastes good or bad, the skin feels good or bad.

The human brain turns as much as possible into black or white; sometimes in an instant, sometimes over years.  Shades of gray or gradations of hue will be added upon recall as time allows. First impressions and gut reactions tend to be kodalithic.

Kodalogic: An heuristic turning all audio, visual, olfactory, tactile, vomeronasal, intellectual, political, philosophical  subtlety to black or white. It is instinctive in humans to do this – probably a characteristic of all vertebrates. We all do it, we’ve all done it. It saves time and perhaps your life. The dog is not well – it is not dead – it’s not going to get well without a $500 trip to the vet – shoot it, thus making it one or the other – alive or dead – in between is expensive. The three young men walking toward me on the sidewalk at night may be angels or devils – probably something in between, shades of gray. I must make a decision to cross the street to avoid them ( they’re devils) or walk forward through them ( they’re angels). Walking in the middle of the street, having split the difference,  would look stupid.

Kodalogic can save your life and it can make your life black and white boring with no subtlety. Kodalogic ought to be used sparingly but it isn’t. Kodalogic gets waay over-used in contemporary America. Overuse of kodalogic is a characteristic of Americans. Kodalogic is so comfortable,  like the latest Lee Child-Jack Reacher novel in which there are good guys and bad guys and the principal  good guy drinks a lot of coffee.

When we are young we see every shade of every sense. As we get older brains turn millions of wonderful, ever-changing-evolving things into  black and white to make room for the necessary facts of life so facts can be easily retrieved. Memories are a file of dehydrated sponges, flat as crepes, wafer-thin, and upon recall they fill out to their fullness and make you happy. Writing a memoir is retrieving a stack of dry, flat sponges all black or all white  and exposing them to clean water to reconstitute them  revealing their color – your wise adult mind is clear, cool water. Look for the humor, the sympathy. Now you see things from mom’s point of view. That evil nun who locked you in the basement laundry room to scrub bed sheets at the orphanage and then pulled you by the ears up to a dinner of overcooked dried out beef liver and mooshy, pale canned peas washed down before gagging with  fizz-tablet root beer served in a scratched up spun aluminum “glass”  has a third dimension. She was the Betty Page of Topeka, Kansas in her youth;  black or white, reasonable or insane. Just add water.



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Packaging Organisms

September 15, 2015

Line up every virus on Earth end to end and they stretch for 200 million light years, far beyond the Andromeda galaxy.  There are10 to the 31st power of viruses on Earth,  ten million times the number of stars in the universe. There are 100 Trillion flu viruses in the body of a person with a three-day old flu. There are 10,000 times more viruses than people on Earth.

There are far fewer bacteria than viruses on Earth, by a power of 10, however, there are many millions of bacterial species on Earth. There are 20,000 SPECIES of bacteria in a quart of seawater and one million bacteria in a single gram of soil. Estimates of microorganism populations vary greatly in the scientific community. By the most conservative estimates there are two million species of oceanic bacteria, four million species of soil bacteria and four million species of atmospheric bacteria.

Scientists have no idea how many viruses and bacteria there are – there are only rough ways to count them, estimates among experts vary to a laughable degree.  There is debate about whether a virus is even a living thing or whether bacteria can be identified as having different species  There is only one single species of Homo sapiens – humans. The human population is a rounding error in relation to the total number of organisms on Earth. The total mammal population on Earth is a rounding error. We are few, like an algal bloom says Lynn Margulis. Here today –  gone tomorrow?

Microorganisms have a collective consciousness. They invented proto-charismatic animals ( animals larger than a wasp) in order to populate emerging ecosystems on a warming earth after the great Sturtian-Marinoan ice age 650 million years ago. Charismatic animals are flexible, versatile, adaptable packages of microorganisms. Each package contains billions of bacteria and trillions of viruses, most of which are beneficial or benign. Fifty percent of the human genome is of viral origin. We are mobile homes to our vast populations of microorganisms. One credible theory of evolution asserts that speciation is caused by the mixing of microorganism genomes rather than by mutation-natural selection and that speciation is not, as Darwin proposed, gradual but abrupt, a punctuation event linking a million generations. Speciation does not appear to be gradual. There is much evidence that speciation happens all at once. Genomes merge, voila ! a new species. Further refinements to the cat, dog, alligator, tuna, Eagle, Bee and Beetle are the result of neo-Darwinian mutation-natural selection but speciation results from mergers and acquisitions.

The Earth is 5 billion years old. Life in the form of reproducing single cells has been evolving for 4.5 billion years. The Earth experienced the second of its 5 major ice ages 850-580  million years ago. The Sturtian ice age covered the entire globe in ice resulting in “Snowball Earth”. Microorganisms lived under a global ice sheet surviving near geothermal vents on the seafloor or in water under the ice. When snowball Earth began to thaw,  an equatorial band of warmer  blue water appeared exposed to direct sunlight. Life thrived here and soon became very  densely concentrated.  A reverse albedo occurred and the ice receded. The close packing of organisms in the narrow warm band of water  forced the merging of genomes. Organisms and their genes merged, fused, incorporated, cohabited, recombined and matched creating an abundance of new species with myriad new capabilities – This emergence of multi celled life forms after snowball Earth  is called The Cambrian Explosion. This explosion of variation on the theme of life occurred between 560 and 540 million years ago. This is the age of trilobites, clams, starfish and snails – our ancestors.

If the charismatic animal is a shrewd, aggressive ambulatory bag for harboring viruses and bacteria, the cell itself was a bag for bits of RNA, DNA for two billion years prior to the Cambrian explosion.  Inanimate amino acids and proteins entered Inanimate globules of fat floating in the primordial soup. Concentrated populations of microorganisms forced mergers during and after an ice age. short strips of RNA squeezed into a hollow sphere of fat. these RNA filled lipid spheres did not multiply by orderly cell division they simply multiplied and the fat globules exploded when they got too full. This was an inefficient way to propagate even though the fatty cell membrane offered a bit of protection from the harsh environment of young Earth.

Inanimate hollow fat globules float around by the trillion in archaic seas. Inanimate nucleic acids, sugars, phosphates, aminos, proteins floated with them, merging in myriad combinations below deep ice sheets up to several miles thick or in equatorial bands of seawater exposed to the sun. DNA strands containing 5 or 15 or 1,500  base pairs get pulled apart and each strand finds  new mates from the freezing, slushy soup of melting snowball Earth – replication!  It’s still not alive. It was an accident. Short strands of RNA attract nucleotides floating freely in the soup becoming double helices – still dead.  A fat glob fills with short strands of DNA a catalyst enters the membrane, the glob breaks into two, some DNA goes left, some goes right. Microtubules enter the scene after they have evolved for a billion years – still no life, a flagellum pushes around a dead glob of fat to keep its head warm.  Another 500 million years of random mixing and matching. A metabolic component here and functional feature such as the light-sensitive protein there. Fat globs fill and explode for 300 million more years – 100,000 fascinating chemical-structural combinations occur –  still no life – no reproduction of the package. Hold that thought – for 500 million more years of random mixing and matching – still dead as a doornail.

JBT –  Rhizomatic design: ( in place of Darwinism, Neo-Darwinism, Creationism, Intelligent Design, symbiosis)  Interaction between organelles, cells, organs cause change-evolution of parts giving rise to wholes.

The man-made machine heuristic; a tool to examine speciation. The taxonomic level of the Order( as in order-family-genus-species) using example of transportation vehicles: space, air, land, water, underwater. Rockets, jets, cars-trains, ships, submarines. Looking closer at the family of aircraft. there are several highly conserved features shared by all aircraft regarding their power to weight to lift requirements. There are conserved features regarding control surfaces: vertical stabilizer, ailerons, flaps.  There are minor shared characters: landing gear and windscreens. The size and shape of the nose of an airplane is the result of many separate contingencies, each with its own map, plans, requirements. There is no specific “gene” for nose shape in an airplane. The nose shape and size are residual – they emerge from the mix. How does one tell a lion from a bear? The shape of their noses is a big cue. The mammal nose is the product of the evolution of 10,000 not-nose elements that evolved over eons in concert with one another. The nose is residual, not a thing in itself, although we see it as such. There is no single gene for noseness.  Take one of many variables: volume. The 747 nose is the result of tens of thousands of decisions around aerodynamics and storage-packing challenges. When a person says they have never seen evidence for speciation i.e. a shared ancestor giving rise to a cat and a bear, this does not mean that one million mutations, all of which have undergone tens of millions of years of evolution have not been stored in the genome for ultimate observable expression as a lion or a bear. Who is to say when a 707 nose will evolve into a 747 nose? Reasons accrue for this expressed difference. More passengers, more need to conserve expensive fuel, longer runways available, stronger lighter materials available for construction. The resulting shape and volume of the nose though not trivial in regard to capacity to smell are minor in the overall causal cascade.

Who can say how many internal, gradual changes occur in one of Gould’s benthic snail fossils across eons prior to a shell’s abrupt vertical extension, his evidence for speciation? The shell shape may be trivial even though it is the only remaining evidence in the fossil record. It should be no surprise that it is an abruption, a punctuation. This shell shape difference doesn’t mean that evolution is abrupt, only that the appearance of the “nosecone” shell distention was abrupt.

Easily identifiable, outward features are conserved while organ system structures and their metabolic patterns undergo constant, relentless, feverish evolution 24/7/365. Why bother with the catness or bearness? Package details are beside the point. It is the stuff in the bag that means life or extinction. It will express at the exterior in the fullness of time if ever.

JBQ – Do methylations, citrullinations, phosphorylations get copied at cell division as they piggyback on the DNA molecule during mitosis during lifespan of an organ?

Madness is often ( always?) equated with unreason. The human neocortex is the seat of our reason. Does a virus interrupt neural links that comprise reason? Do viruses clog the rhizome of reason?

JBE ( Experiment) – Study effects of 100 species each of virus, bacteria, worms and protozoans on 25 brain areas re: mental disorders. This involves 10,000 labs around the world for two years. Let’s find out how many mental disorders of the DSM-5 big 900 are caused by microorganisms. A hysterical man sits in his psychiatrist’s office with a brain infected by tapeworm cysts driving him to madness and the shrink asks to hear about the poor man’s relationship with his mother.

What are the VBP ( viral, bacterial, parasitic) effects on neuron-synaptic electrochemical communication? Can a single virus short-circuit a synapse? Perhaps a single virus can extend the gap between synapse ends thus making it impossible for electrical charge to pass this juncture thus stopping an afferent or efferent nerve impulse in its tracks. Identify chemical exude of 100 species of virus – test their effect on the following: neuron firing, neuron signaling,  ability to form new thoughts, connect new thoughts to one another and to memory, connect sensation ( visual, audio, tactile, vomeronasal, taste) to memory, to connect sensation to reasoning ability, to higher levels of abstract thought – morality, ethics, altruism, math and language skills.

To Do: In examining those with mental illness: 1. Check for VBPs 2. Once the VBP has been identified after searching for many species,  remove them.

JBQ – does viral DNA penetrate neurons? Is there a toxic viral exude with negative effect on cognitive function? Same for bacteria and worms. A brain is infected with pinworms, roundworms, schistosoma or tapeworms would be subject to physical dislocation of brain mass and suffer the effects of worm waste and the effects of its consumption of brain matter i.e. the total metabolic impact of the parasite.

JBQ – Is madness  the result of the human brain testing an array of potential advantageous effects of viral, bacterial, parasitic involvement in brain function? If it helps – keep it. If the potential symbiont or gene sequence doesn’t help ( see: “madness”) omit it.

JBQ – Were the hippocampus, thalamus, cerebellum, pons, globus pallidus, putamen and amygdala once upon a time parasites of our archean neural nodules that  proved useful? they each now have  a unique structure and purpose in the brain having evolved from a tight little club of parasites formerly swimming freely in the Silurian sea. Each symbiont provided a selective advantage. Fish to itself “I’m going to have to begin coughing once I crawl up onto the land I’d better keep this little parasitic knot of cells ( future Medulla oblongata).

JBQ – what microorganism initiated the tendency in vertebrates to aggrandize one’s self, to strut around and flash feathers, sing, dance, howl, growl and roar? Drawing attention to one’s self was once considered madness among humans in  medieval times and is now rewarded in all American children? “Raise your hand ( separating yourself from  your classmates)  if you know the answer.” What virus removed our fear of standing out from our fellows removing our prehistoric fear of being a tall poppy? Toxoplasma gondii virus removes fear of cats in mice. FACT: viruses are known to make certain types of fear disappear in some mammals. What viruses,  what fears in humans?

JBT – If fear expression is the result of a methylated histone, perhaps a virus de-methylates this histone during lifetime, thus epigenetically reducing  fear in a small segment of the population. This fearless population is our avante-garde. A deme’s fearless pioneers. Were pioneers of the Oregon Trail all infected by a midwest virus that reduced their fear of the unknown and or initiated wanderlust? Same question for Jamestown settlers, Pilgrims – all emigrants to North /America in 17th-20th century. Catch a virus – go directly to the New World, sever roots and explore, thus participating in a viral evolutionary experiment on the human brain. Get these brains out into new ecosystems for viral-bacterial proliferation. Do viruses remove fear in bacteria or larger parasites? Do worms feel fear? Are protozoans afraid of anything? If viruses are experimenting with the human brain, as humans set out for parts unknown, what part of the brain is involved? the neocortex, amygdala, brainstem, hippocampus? Travelling to the New World in the 17th century was definitely crazy-dangerous and wrought with doom.

Michel Foucault and others assume that human reason emerged during the Renaissance and came to flower during the 18th century – the “Age of Reason” These thinkers imply that ancient times and the Dark Ages were bereft of reason. This is a misconception. Every age is filled with as much reason as any other. The architects, engineers and administrators of ancient Mesopotamia, Egypt, Greece, Rome and Gothic Europe were obviously reasonable men. Reason wasn’t invented in the 18th century by Voltaire and David Hume. It simply became more fashionable among a noble few as reason became a meme.

JBQ – Does DNA have more than one way of quieting or erasing a trait? Imagine a word you have written on paper – you can erase it or scratch it out or scratch it out and then cover up the whole mess with white out. Does the cell have a 2 or 3-tier system of gene suppression? – the scratch out, the cover-up and the erasure? Are there various levels of removal? Erasure from operation during a lifetime and erasure from the genome at germ cells i.e. gone forever. Once a gene has been omitted can it be reinstated a million years or a day later?

JBQ – Are viruses the primary mechanism enabling the evolution of human consciousness? Do viruses stir the cranial pot putting behavioral options on the table for natural selection – social selection? Are memes  inherited via changes to neural chemistry? or simply learned / absorbed from parents, friends, teachers, television and the internet?

JBE – Explore viruses as DNA mutagens in the manner of UV radiation or traditional Neo-Darwinist mechanisms for mutation.

JBQ – How would the human brain conserve a positive viral effect on social behavior or any behavior?  Is altruistic behavior, a notoriously counter-intuitive animal trait, a virus-borne aberration that has proved beneficial to the species, thus conserved? If so, by what chemical process and reproductive pathway? A proposal 1. Virus rearranges neural protein at amygdala 2. this modified protein geometry is somehow relayed to germ cells.

JBQ – Is melancholy a viral affliction? Melancholy, a recognized mental ‘illness” of the 16th-19th century,  recast as depression in the 20th.

JBQ – Are Conservatism and Liberalism caused by different virus species? If so, can either be cured?  Is religion a species-wide microorganism infection?

JBQ – Does inheriting a virus via sperm-head  epibontics (piggybacking) have the same effect on a new life as if that virus caused a mutation at the DNA or initiated a heritable post-translational modification? Are the effects of a specific virus identical, independent of method of transport into new life? Are effects different and are the effects related to their means of arrival?

  1. Epibontic transport of virus “X” causes disease “A”
  2. Base pair disruption from virus “X”  causes disease “B”
  3. Virus “X”  initiates a histone phosphorylation that is inherited via “junk” DNA or inherited via  a protein-coding gene causing disease “C”

Bottom line proposal: One virus may cause multiple health outcomes, for instance:  “A” affects hippocampal function – long term memory “B” erases fear at amygdala “C” affects the nature of Structuralist language capabilities such as inborn tendency to comprehend  grammar or ways of organizing the visual field re: size-closeness.

JBRT ( Russell’s Teapot logic: I can say anything and it’s up to you to prove me wrong – Bertrand Russell asserts that his teapot is orbiting Mars – he dares you to prove it isn’t.) All aspects of human consciousness, self-awareness, behavior, language, altruism, social skills  that are related to the emergence of our outsize neocortex are initiated and modulated by microorganisms and resulting  long term advantages are locked into the human genome  by the acquisition in our DNA of viral, bacterial genes or by permanent and heritable post transcriptional modifications.

JBT – Mental illness is the ( now negative) manifestation of unprocessed, viral-initiated neocortical options presented by nature for possible use in future generations to positive social effect.  It was crazy then – it’s normal now.  This happens all the time. As new behavioral  options become manifest in people,  this unique  behavior, that could have 100 different names, is all classified as schizophrenia.  To Do: Look for 100 sources for 100 unique behaviors now all lumped together by psychiatrists as schizoid.  Look at schizoid behavior as a source of new possibility for mankind.  As in all evolution,  99% of the new is rejected outright. We are surrounded by the surviving 1% aka 9 million successful animal species. Nature makes an enormous number of mistakes. If one percent of schizophrenics manifest a productive behavior they are par for the course. Crazies are an important  source of human evolution.

JBT – The gradient between reason ( the sun) and madness ( the cold dark void) is modulated by living organisms. A listener advances on madness with language. Language is life. Language modulates the gradient between madness(bliss) and reason.

Find a gradient and reduce it for money, fame and glory.

JBQ – What social gradient did Rock and Roll reduce? Was it strictly the gradient that always exists between adjacent generations and always subject to reduction or was there more to it? Rock and Roll reduced the terrible gradient between Black Americans and White Americans post JIm Crow,  paving the way, more than any social force,  for civil rights. Norman Mailer reduced the gradient between hipsters and squares.

“Random mutation hones already extant species that originated via symbiosis”-Lynn Margulis, Dorion Sagan

JBT – It is said that a gene has so and so number of base pairs yet the mechanism for transcripting-translating genetic information involves RNA reading the code off of one side only of a DNA molecule separated down the middle. The two sides of this sequence of now split apart base pairs, each side ( each column of bases) carry genetic information. Seems like one side of the DNA sequence could code for eye protein and the opposite side for glomerular cells ( kidney filters) so it’s never base pairs that code but rather sequences of bases stacked on one side of the now opened double helix.  A gene does not have a number of base pairs. It has a number of bases – 3 bases per codon not 3 base pairs per codon. Verify. I’m failing to understand something here. It’s base(ic).

Analogy – Imagine a copy of “War and Peace” in your left hand and a copy of “Infinite Jest” in your right. Now shuffle these two doorstops like two decks of cards – this is a section of a strand of DNA. At transcription the pages of the two books are separated so that RNA has access to one of the books only ( say “War and Peace”), to one string of letters, one series of codons ( not both -as they are no longer linked at the center as base pairs but simply as strings of bases) The RNA reads from either “War and Peace” or from “IJ” not from both simultaneously,not from base pairs – just a sequence of bases. Genes are always characterized as having so and so number of base pairs when actually they are so and so number of bases – no pairs at this point and time of transcription. If the human genome has 3.2 billion base pairs wouldn’t it have 6.4 billion  letters to work with? 3.2 billion bases per side of the double helix? Someone tell me what I’m not seeing here.

JBQ – What are the genes that govern our power to reason and dream? Perhaps not genes at all but methylations locked into heredity.

JB Universe model: 1.  Imagine a sine wave at 30 to the minus 15th power  cycles per second 2. Rotate this continuous wave to form a long series of pulsing  3-D volumes – expanding-narrowing-expanding 3. Now pack countless waves  adjacent to one another, slipped for a snug fit. One cycle in one wave is our universe and we are halfway through our own cycle like a wave passing thru water – time being the wave and the universe being the water. 4. Bundle countless waves adjacent to one another out to infinity – like a muscle and its fibers, one fiber being the history of our particular sequence of universes-pulses. One pulse takes 30 billion years. Our universe is at the midpoint of its cycle.

Filling a primordial cell membrane after the Huronian global ice age 2.4 billion years ago was like filling a shopping cart while pushing it through ancient pet shop-nursery. “I’ll take some of these and some of those.” The wonders that grew from these early associations!….in ten million shopping carts.

The immune system and the cell membrane work together to prohibit entry of viruses into the organ cell. the membrane is the wall with many closely guarded portals the immune system is the military chasing down terrorists and killing them before they enter the cell. Does a cell membrane prevent the operation of the organism immune system i.e. does the cell membrane protect the virus from phagocytes once inside? Is the cell a safe harbor all viruses, friend or foe?

JBQ – Does DNA really split down the middle when it replicates during mitosis? Is splitting really necessary? It makes a cool explanation but does it really replicate in this way? Could DNA double helix not remain locked and activate a switch to attract like bases from the cytoplasm? It turns switches on and off for 1,000s of other DNA functions-processes why not replication? Stay locked into a double helix and signal moment for replication when free-floating nucleotides form a mirror molecule that floats away on its spindle?

JBQ – what percentage of a DNA molecule spreads apart in order to be copied by RNA during transcription in a specific organ tissue – kidney, liver, heart, etc.?

JBQ – Do we catch diseases when invaded by microorganisms or do we catch environmental toxins that destroy our resistance to organisms already present in our bodies?

Organisms hijack one another’s DNA. Viruses and bacteria are promiscuous. They are continually swapping DNA with one another and among themselves and higher organisms such as vertebrates. Half of the human genome has its source in microorganism DNA.

Evolution means: annex, attract, amend,  absorb,merge, fuse, co opt, convert, incorporate, encompass, cohabit, combine, recombine, integrate, interface, tie-in, throw-together, hitch on, hook up, team-up, tack on, tie-in, transfigure, transform,  plug in, bind, bond, blend, unite, absorb, swallow, subsume, meet, mix, mingle, marry, meld, merge, centralize, coalesce, converge, conjugate, consolidate, conjoin, cohere, fuse, federate, join, meld, weld, enfold, amalgamate, amalgamete! assimilate, agglomerate, transmute, re-style, re-fashion, revamp, revise,  remodel, re-cast, re-shape, shack-up, play house… infinitum…..oh !…. and DNA mutation.


  •  September 15, 2015  2:29pm


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Memes, Demes and Genes

September 6, 2015

Meme: An idea, behavior, style or usage that spreads from person to person within a culture.

Deme:  A local population of closely related interbreeding organisms

Gene: A sequence of nucleotides in DNA or RNA. The gene is the functional unit of inheritance controlling the transmission and expression of one or more traits or metabolic processes by specifying the structure and composition of a polypeptide, especially a protein. The gene may also control the function of other genetic material.

Meme example: Neo-Darwinism i.e. organism evolve via genetic mutation – natural selection

Deme example: The population of scientists who believe adamantly  in neo-darwinism

Gene example: The genes for catness vs dogness or bearness. It’s in the ears, snout, movement, color, size

All learned components of human culture are memes: language, cultural norms, widely shared notions of justice, sanity, ethics. Each deme has its version of the memes. For a catalog of demes from around the world see: “The Savage MInd” by Claude Levi-Strauss. Memes change, evolve, devolve. There is a hierarchy of meme causality from the larger changes in law of land to trivial changes in hairstyle, music, art. Memes form a rhizomatic shared consciousness among people.

The human gastrointestinal tract is home to ten trillion bacteria. They are a vital part of digestion. There are 60 virus phages for every single bacterium. Each of these organisms contains its genome.  Our bodies contain 1,000 demes of microorganisms, each with its meme- rhizome interconnectedness with neighbors. The human genome with its 20,000 genes is a tiny fraction of the operative genome in every human body. We live with a Ka-trillion genes – too many to count – all working together for our health or not working together,  causing disease. 

Were our organs early symbionts? Entire creatures that specialized in blood filtering, fat breakdown, Oxygen-blood transfer, pumping, various hormonal capabilities that have merged into a single animal that evolved as these systems became adjusted to one another and to different environments over eons – over one billion years? Archaic kidney as an acquired entire genome working with others of the sort with 99% of evolutionary time being used for internal inter-system coordination distant from the light of day; like a busy engine room in a cruise ship i.e. traits are expressed and subject to natural selection without confronting another species. This internal selection occurs over thousands of generations of cell growth-death-birth in the life of a single organism The creature they called the swimming liver is long extinct. A billion years ago there were a million different single cell organisms each with a specialty: thinking-connecting,filtering, pumping, fat metabolizing – mix n’ match across eons. Much of the heavy lifting of organ system coordination occurring when the systems were simple, primitive, pliable, flexible. First organelles  merge then a billion years later the organs merge – two distinct levels of organization: intra and inter-cellular with the gene-switching capabilities of viruses and bacteria lubricating the emergence of complexity.

Symbiogenesis: Long-term stable symbiosis that leads to evolutionary change.

All characteristics are acquired – JB

What was the first animal to have all of the following: heart, liver, kidney, lungs, neural cluster.

Stomach cells have a nine day lifespan, 40 generations of cells per year over 80 years. 3,200 generations of stomach cells in a single lifetime. It would take 80,000 years for an equal number of human life generations at 25 years per generation. Most evolution happens at cell level as  systems coordinate and evolve together in a million different species. Stomach cells receiving epigenetic signals for immediate expression from hundreds of organ components and metabolic processes as organs adjust to the lifestyle of a specific person and to their own development as systems throughout the entire body prior to germ cell involvement for effects on heredity i.e. DNA adjustment.  3,200 generations of cell division using epigenetic tags for gene expression-modification independent of DNA mutation. These intra-lifespan changes are from sensory-chemical signals with sources throughout body not from solar radiation or environmental mutagens.

Effects of environmental mutagens on intra-lifespan phenotypic proteinic expression-regulation i.e. a cell deme at an organ gets derailed genetically say via histone poisoning that is then epigenetically heritable within lifespan ( 3,200 generations) of individual  independent of sexual reproduction of entire organism. Genes get modified, mutated, disrupted as well as coordinated, refined.

Coorganation: the evolution-coordination of organ systems and metabolic processes among organs via epigenetic ( post-translational) modification – heritable within a single lifespan. Coorganation can be slowed, interrupted by environmental mutagens, toxins. Affect one organ and you affect them all.

To study: Ratios of inter organ effects. Example: I poison liver-kidneys with alcohol; what coorganate signaling is negatively affected at the following organ systems: brain, heart, lungs, endocrine, immune. does cell trauma at kidneys signal neurons at pons to phosphorylate?

Given Neo-Darwinian mechanisms of mutation-selection and observed species evolution, there has not been enough time by a factor of 1,000 for animals to have evolved into present forms from Earth formation from orbiting dust. Thus the argument for coorganation – intra-life mutation-selection cycles.

The modification of a gene is a big deal and the body has sophisticated systems in place to prevent it – DNA repair, cleansing. A mutation is a big deal if it signals an improvement in the system. This novelty gets played out 1,000 times prior to formal encoding in DNA for transfer via germ cells at germ cell genome.

To do: analyze the human  “genome” at 20 cell types throughout life of an animal – are the genomes identical in all 20 cases? probably not as each organ system is accruing its changes through hundreds of cell divisions. How are these distant changes assembled in the germ cells? Do viruses or bacteria relay genetic info to germ cells as they accrue. Do we have messenger viruses that act as relays between heart, lungs, liver, kidneys and germ cells?  Some mechanism for keeping sperm up to date with latest  organ improvements in the event of a DNA transfer via sex?

Explore: the ratio of intra-life coorganation beneficial mutation events to actual heritable base pair changes-mutations. Is it 10,000 to 1, 100 to 1 would be a lot.

JBQ – How would the advantage of longer fangs get worked out at intra-life level if only one set of teeth per life? Answer: It wouldn’t – some things must undergo whole-life generational testing and perhaps 1,000 of these much longer organism generations. Advantage of longer fangs is a gross example – look for the advantage of one of 500 folding options in a protein that acts as a molecular gate at membrane lipids.

Who-what-how is intra-life coorganation performed? Is it all done via chemical signaling? Is there an area within the limbic apparatus that acts as a command center for these options at distant organs? A zone of judgement at the brain or does each organ system have its own judge-jury- executioner. “This is an improvement” “This is not an improvement” you die ! One of 100,000 options tossed onto the evolutionary trash heap in a single mammal lifespan.

what is the role of viral-bacterial DNA-RNA etc. in coorganation? A non-pathogenic virus can visit every organ in the body in half an hour and relay info back and forth between systems, deposit chemicals, new proteins, enzymes, fats.

JBE – Look for intercell messengers between organs and germ cells. How are hard-won evolutionary advantages at organs relayed to germ cells as novel  heritable traits? How does the organism avoid wasting the benefits of hundreds of generations of evolution at billions of cells?

According to neo-darwinist dogma,  only mutations at germ cells can be transmitted to a new generation producing a mutant swerve for testing via natural selection.

The great speciations occurred in deep pre-cambrian epoch a billion years ago as symbiotic aggregations took root then forever after until the present,  it’s all coorganation. Most evolution is internal as organs evolve and coorganate with one another with their highly conserved foundational genes locked in where they are protected from casual mutation.

A three week old human fetus replays-expresses renal features it has remained in touch with for 500 million years for the first 3 weeks after fertilization then – “oops” not this one! as the pronephric proto-kidney dissolves allowing the mesonephric version to develop for 5 weeks – no go ! not this one either. Finally, on the third try the metanephric kidney develops and it’s off to the races for life.

JBQ – Is the prostate a command center for the relay of epigenetic information from all organ systems to sperm cells? Is there an analog in females? Does nuclear DNA at sperm dematerialize into chromatin? Is there a daily cycle of receptiveness when new genetic info is added to latest batch of sperm. To do: Look for chromatin cycles at germ cells.

JBQ – where are the free-living mitochondria ? Have they gone extinct?

JBT – Seems like mutations at vomeronasal chemistry would most likely cause interruption in mating continuity leading to sexual isolation – speciation. New mutation doesn’t  pass the smell test. Is vomeronasal change inherent in all speciation?  Who could know? There has been no new species evolution observed – ever.

JBQ – Why would a bird care if its mate had a red-tufted head or webbed feet if the pheromones were still attractive and why would it mate with a look alike if vomeronasal chemistry had changed?

Note:   All myth is truth – all truth is myth.

“Speciation is a property of nucleated organisms. Speciation began with the earliest protoctists 2 billion years after first bacteria and viruses.” –  Lynn Margulis

JBQ – How do newborn animals depending on a diverse microbiota in their gastrointestinal tract and many other locations, restore, reanimate the wide variety of bacteria and viruses during gestation-birth-life?  It can’t be all via mother’s milk.

JBQ – How much non-human DNA ( viral, bacterial) enters an ovum at fertilization? Does this new generation of microorganisms  hitch a ride on the surface of sperm head or sperm mid section? We now know that mitochondria travelling in sperm midsection enter the egg, contrary to widespread previous belief. How much viral DNA is carried inside the head of the sperm to grow along with blastula-fetus into new life?


9/6/15   3:57pm

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