Tuesday, September 20, 2016

THE SHAPE WE'RE IN


  


TIGER, tiger, burning bright
In the forests of the night,
What immortal hand or eye
Could frame thy fearful symmetry?


                            William Blake. 1757–1827

Alas, poor William.  If only he were born in this century, or even the last.  Then he wouldn't be filling his head with such foolish speculations.  Or if he did, he wouldn't dare express them.  Imagine the scorn, the contempt, the mockery, that he would receive for bothering himself with such frivolous wonderings from the likes of Bill Mahr, Christopher Hitchens or Richard Dawkins.  These three and other such like minded enlightened people would pity the naivety of a human being awestruck by the power and beauty of design in nature.  But perhaps it is all understandable since it wasn't until the late nineteenth century,  that all these mysteries were unraveled and that we now have, courtesy of Charles Darwin,  a real and thorough understanding of how we, and all life forms, arrived at the shape we are in.

Or have we?  The neo-Darwinian understanding of the origin of all the marvelous shapes that we (and by we, I mean all life forms) find ourselves in, is that it was arrived at  through the mechanisms of mutation (replication errors in the copying of genes) and natural selection.  By the workings of these two processes, very gradually, advantageous mutation by advantageous mutation, all the myriad and wondrous shapes of life have been arrived at.  It's so simple, isn't it, once the truth is known?  Yet I have a few small quibbles with these 'foundational' truths that are accepted without question by the Church of Neo-Darwinia.

What  relationship is there between genetic mutations and shape? Regarding the shapes of organs and whole bodies, probably very little.  Even the ability of a genetic mutation to change the shape of the protein molecule that it is coded for in any useful way, is called into question.  As protein structure has become better understood, it is now known that the protein is folded into certain shapes, with one hundred or more amino acids involved in each fold.  Also, the shapes and folds are constrained by the chemical qualities of the amino acids.  Some acids are positive, some negative; some bind with the water molecules in the cytoplasm and some are repelled from the water of the cytoplasm.  Biochemist Douglas Axe has shown that the chances of arriving by random mutations at a new protein fold, which would be necessary to not merely adapt the function of the original protein to different surroundings without changing its function, but to actually add a new useful function to it, are so small as to be inconceivable.

Also proteins are sub-microscopic.  Perhaps a million of them  occupy each of the 37.2 trillion cells of our bodies.  How could something that tiny effect the 'fearful symmetry' of the tiger?  In fact with all the 'proof for evolution,' the only mutational changes that have been found to have any benefit at all are chemical changes, not shape or morphological changes.  Neo-Darwinists, as much as they would like to claim and do claim that the basic mystery of life has been solved and we are now merely working out the details, are at a loss to name one advantageous morphological change caused by a mutation.  If they are pressed, the one that they come up with, the one change that they can name of the trillions upon trillions of mutations that would be necessary to begin to achieve the myriad shapes and shapes within shapes of all modern organisms, is the change in shape of the hemoglobin molecule that comes from the mutation causing sickle-cell anemia.  Yet even this one change is clearly not  an improvement of shape, but a degradation of shape.  In malaria infested countries people with one sickle cell gene have some advantage in surviving malaria.  They do have mild anemia.  In fact, if they had two sickle celled genes, they would have severe anemia and probably not survive past  early childhood.  With one such gene they have sickle cell trait rather than sickle cell disease.  This means that because of the degradation of the hemoglobin molecule, the naturally rounded shape of red blood cells collapses in on itself causing a 'sickled' cell.  This shape is less efficient in transporting oxygen around the body, which is the reason we have hemoglobin molecules (our body, amazingly, produces one hundred trillion of them every second), but it also makes it impossible for the malarial protozoa to breed within these sickled cells.  The malarial protozoa gets trapped in collapsed, sickled red blood cells and these cells are recognized by the body as antigens and, along with the trapped protozoa, are eliminated.  So, in heavily infested malarial areas of the world, since people with one copy of this sickle cell gene tend to survive malaria while those who lack that gene often die of malaria at a young age, the sickle cell gene survives.  This is a process of Darwin's natural selection at work, but it is not a process that would lead to any kind of evolution, or 'improvement' from one species, or one class or one phylum to another.  In fact, if left unchecked, it would lead to extinction, because if the majority of any population carried the sickle cell gene then more and more people would inherit the gene from both parents and would have sickle cell disease and die of severe anemia before the age when they are able to reproduce.  So natural selection here is both assuring the survival of the sickle cell gene in malaria infested areas and limiting that survival by killing off inheritors of two sickle cell genes.  It is adaptive, as natural selection based on random mutations always is, in that it allows organisms to cope with environmental threats; but it is not evolutionary, in that natural selection based on random mutations never produces any morphological change that would lead to the development of new species, new classes, new kingdoms, or new phyla of organisms.

Mutations may cause chemical changes which are beneficial to the digestive and immune system because these systems depend on the shape of specific amino acids within the protein molecule to bond with food molecules and pathogens in order to work.  Regarding the shapes of whole organs and organelles and tissues and body symmetries; genes and their protein products are way, way too small to effect any change at that level.  That would be like saying that the shape of grains of sand determines the sand sculptures that you can make with them, or the shape of the tiniest pixels in our modern technology effect the shape of the pictures that can be composed using those pixels.  In fact, in metazoic (multi-celled) creatures the same genes creating the same proteins are used by themselves or in combinations with other proteins in a whole range of different body parts and are themselves involved in the maintenance and structure of many differently shaped parts within the same organism.

Remember Gregor Mendel, the first geneticist and his experiments with peas?  From reading about these Mendelian experiments we got the impression that one gene equalled one trait.  One gene would create a certain kind of petal and another gene would create a different kind of petal.  Understand that Mendel's breeding experiments came way before the discovery of DNA and the understanding of genes and proteins that we now have.  Actually traits are created by clusters of many, many genes that are swapped during sexual reproduction.  Any trait that is noticeable, that doesn't require high tech chemical testing to detect, but is an actual change of shape, requires the interplay of dozens of proteins which, in turn, requires the alteration of staggeringly complex embryological gene firing patterns and unfathomably complex changes in the system of embryological cell differentiation and cell migration, to say nothing of changes in the circulatory system to get nutrients and oxygen to that new trait, changes in the nervous system  and brain real estate so there is a control center for the maintenance of that trait, changes in the skeletal system and the musculature, so there is physical support for that trait and equilibrium is maintained, and on and on.  The simplicity of the neo-Darwinian formula: copying errors in gene replication + natural selection = the myriad variety and complexity of modern life, depends on a naive, out-dated, Mendelian understanding of genetics, and a complete disregard for the overwhelming complexity and synchronicity of embryological processes.

Many evolutionary biologists still cling to the idea that DNA contains all the information necessary for the growth, shape and maintenance of living bodies.  They point to discoveries of networks of regulatory genes which are recipes for proteins that, once manufactured, re-enter the nucleus of the cell and stimulate or suppress the expression of other genes.  Early on in the embryological process, genes are expressed that produce proteins that regulate the expression of genes in different parts of the body.  Somehow, within the initial cell, the fertilized ovum, there is a magnetic polarity, so that certain regulatory proteins are distributed unevenly through that ovum.  When the ovum mitotically divides, the daughter cells have different distributions of these proteins, so different genes wind up getting expressed in different cells.  It is fascinating and wonderfully complex and goes a long way toward explaining how different types of cells are distributed in different directions as the morula, the sphere of daughter cells caused by the mitotic division of the ovum, develops.  It tells us nothing about how or why the morula develops into the blastula and then the distinctive shape of the gastrula, distinctive for each species, and then the further migration of all the cells.  What is sort of explained is how the cells are initially differentiated into different types of cells.  I say sort of, because we know nothing of how that particular magnetic polarity in human eggs gets there and how or why it differs from the magnetic polarity in chicken eggs or frog eggs or monkey eggs.  Then, once we wind up with different cells, where is the control which determines how much of each cell is replicated, when it is replicated, and how the different cells are migrated in different directions once gastrulation and the further development of body parts is accomplished?
                                                                                                                  
                                    STRUCTURALISM

Structuralism was the predominant scientific position regarding body formation prior to Darwin, and is currently enjoying a fairly robust resurgence.  It holds that organic matter,  just like inorganic matter, has certain inherent properties and the forms that it takes in charged, metabolic environments, is predestined by these inherent properties in the same way that the shape of atoms, crystals or snow flakes is inherent in the chemical and physical properties of those particles.  That does not mean that there is no variation of shapes among atoms, crystals and snow flakes,  but that there is a basic, underlying shape or pattern that is invariant.  This basic, invariant pattern is what Richard Owen, one of the giants of structuralist biology, called the 'primal pattern.'  The variations on the primal pattern were referred to, by Richard Owen, as the 'adaptive mask.'  For instance, the atom always consists of a central nucleus which, in turn consists of some combination of protons and neutrons and  some combination of electrons that circles the nucleus at a considerable distance from it (considerable in relation to the size of the nucleus itself).  This is the invariable primal pattern, but within this pattern there is variety in the number of protons and neutrons that make up the nucleus, the number of electron particles  and the distance at which they circle the nucleus; all of these variations deriving from the environmental factors at the time the atom was formed.  In the same way, crystals expand into a very wide variety of shapes depending on environmental factors during this expansion, but they achieve this growth using a much more limited variety of repetitive patterns,  those primal patterns being dependent on immanent chemical and physical qualities of the elemental or molecular material that is crystallizing.  All the distinctive patterns that make a crystal recognizable as a crystal, an atom recognizable as an atom, and a species recognizable as a species, are the invariant primal patterns, and all the specific qualities that make a crystal a particular, unique crystal; make a snowflake a particular, unique snowflake, and make a member of a species a particular, unique member of that species, are the adaptive mask.

We are referred to as 'carbon' based life because of the central role that the carbon atom plays in nucleotides and proteins.  Structuralists remind us that  not only the carbon atom but  the oxygen atom and organic compounds, like carbon dioxide and water,  have certain inherent properties that allow them to combine in ways that create the complex chemical systems associated with life and without which there would be no life.  These properties do not change over time, are not responsive to environmental variations, and as such are beyond the purview of genes or adaptive changes.  They are epigenetic and come from inherent properties and laws that are imminent in these atoms and compounds themselves.

These immanent and unchangeable qualities of matter, both organic and inorganic, were thought of as being part of a Divine Plan, with no more explanation to it than that,  that I could find.  The adaptive masks were somehow adapted for different environments and uses, but that process was also not elucidated.

                                    FUNCTIONALISM
                                                     
The spread of Darwinian thought put an end, at least temporarily,  to the idea of living organisms as natural outgrowths of chemical and physical laws.  Darwinian organisms were considered artifacts, consisting of components randomly cobbled together as the chance outcome of accidental mutations and the natural selection of an arbitrarily changing environment.

As Michael Denton writes,
"The adoption of the 'contingent mutable artifact' as the metaphor of organic form ushered in the modern era of biology and changed the whole explanatory framework of biological science, from what was a structuralist/functionalist (primal abstract patterns by law, adaptive masks by environmental selection), to a purely functionalist conception of nature.  The very naturalness of life-the idea of life as a necessary part of nature-was abandoned.  The metaphor of the crystal was replaced by that of the watch." 

With the unquestioned, almost monolithic, acceptance of Darwinian thought, the ubiquitous presence of epigenetic, unchanging and non-adaptive patterns in living organisms have been overlooked, until recently.  The entire system of protein manufacture including the processes of transcription, translation and DNA replication is one of those patterns.  These highly complex, highly precise functions, all operating synchronously and in tandem,  and all operating in every one of the 37.2 trillion cells in your body at this very moment, are the system by which all the protein molecules needed for the construction and maintenance of living organisms are manufactured and supplied, and are, in their essence, and aside from the addition of a few bells and whistles, exactly the same processes that manufactured and supplied proteins to the first chemotrophic and photosynthetic bacteria that began life close to four billion years ago.  Although we still are not close to understanding all the processes that are involved in the functioning of such remarkably complex apparatus as the protein transcription, translation and replication equipment, it is hard to the point of impossibility to imagine that all of this arose simply in response to environmental factors.  In fact the whole Darwinian theory is based on viable, already living organisms,  gradually developing features that enhance their survival.  Yet without that equipment, an organism, if you can call organic material lacking the means of manufacturing proteins an organism, is not surviving anyway, so there is no basis to select  a feature that helps it to survive more and drop a feature that helps it survive less, when there is no survival going on in the first place.


Although we cannot explain entire biological systems in terms of immanent laws, we certainly can explain many essential aspects of them by those laws.  The nucleotide chains of both DNA and RNA consist of an invariant backbone of a five carbon sugar and a phosphate base, which combine with each other and attach to new nucleotides  in always the identical manner (the primal pattern).  Nucleotide chains also contain a base, always one of four possible bases, and the various arrangements  of these bases is the adaptive mask. It is this very variety of nucleotide base arrangements that contain the information of the genetic code.  Yet while there is necessary variety in the way the bases are arranged on the original strand, there is no variety in the way the bases are arranged on the opposing strand.  The bases line up on opposing strands in a manner that is  invariable and absolutely constant, regardless of any environmental contingencies:  A (adenine) to T (thymine) and T to A, and C (cytosine) to G (guanine) and G to C in DNA, and A to U (uracil) and U to T, and C to G and G to C in RNA. This consistency is due to their physical shape and chemical composition, so when they are opposite each other and in the correct position they form hydrogen bonds which hold the two strands together.  This is another part of the 'primal pattern' of DNA that does not change regardless of the  class or phyla or kingdom that an organism belongs to,  and has not changed or adapted in any way over the millennia.  So this too is epigenetic, beyond the influence of genes and is immanent, based on internal physical and chemical laws, and does not alter with alterations in environmental factors.

Also, the way that proteins fold, into variations of alpha helices and beta sheets,  are determined by the chemical nature of the proteins and their response to the watery environment of the cytoplasm.  These folding constraints may limit the number of possible mutations and create huge hurdles for neo-Darwinian contentions that all evolution is the result of the random appearance of new proteins.  Proteins may be found to have a history that is more limited, more cyclical and repetitive than open ended and revelatory, because of the physical and chemical constraints involved in the protein folding process.  In other words, evolution has more likely taken place,  not from the chance arrival of novel proteins, but from combining a limited vocabulary of proteins and using them in novel ways.

Lipids have also been discovered to be self organizing in an aqueous solution, according to their chemical properties.  Lipids have a water averse, hydrophobic side and a water loving, hydrophilic side.  In water, they self-organize into bi-layers with the two hydrophilic sides on the outside and the two hydrophobic sides protected from the water and pointing inward.  These bilayer lipid membranes form the outer boundaries, the membranes, of all living cells and the boundaries of organelles within the cell, including the outer membranes of the nucleus, the mitochondria, the chloroplast, etc.  Now they can be adapted, bent and re-shaped by proteins to fit specific adaptive needs, but, again, this is the adaptive mask altering the primal pattern which is epigenetic, obeying inherent chemical laws and not responsive to adaptive neccessities.

Finally, there are the deep homologies that, although they have always been claimed by Darwinists as evidence of their theory, actually give convincing support to the structuralists.  The same basic patterns and shapes appear in a wide variety of organisms, both plants and animals,  and have been adapted for a wide variety of uses.  A most famous one is the one-two-five pattern.  In tetrapod limbs, whether they be legs, arms, flippers, fins, or wings; whether they be used for swimming, flying, jumping, running, pollen collecting or grabbing prey; they follow the same pattern of one larger, thicker bone (in humans, the humerus of the arm and the femur of the leg) leading to two bones (in humans, the radius and ulna, leading from the elbow to the wrist, and the tibia and fibula, leading from the knee to the ankle),  and then separating into five bones (in humans. the metacarpals of the hand leading to five fingers and the metatarsals of the feet leading to five toes).  Yet what has been learned about this homology is that it is produced in different organisms with completely different genes and following completely different embryological pathways.  In other words completely different manufacturing techniques, consisting of completely different genetic pathways, wind up with the same one-two-five pattern. So this pattern (the primal pattern), although it has been modified over and over again (the adaptive mask) has endured in all it's various forms for hundreds of millions of years.  The form, the primal pattern, is adapted but never sacrificed.

The same holds true for all the other deep homologies.  They are arrived at through different genetic paths and different manufacturing techniques, even formed from cells deriving from different embryological tissues, but somehow that basic pattern winds up being constructed.  Where do these persistent patterns come from if they are not derived from either the genes or the embryological body plan and the migration of particular cells?

                                     EPIGENETICS

I need to mention here a number of fascinating discoveries made recently concerning the epigenetic (beyond genes) processes of cell formation and cell to cell alignment.  These discoveries include the understanding of how changes in microtubule structures within a cell change the shape of a cell; that the same cell's shape can change during the life of that cell and that microtubules which radiate out from a centrosome near the nucleus of the cell to the periphery, along with actin filaments, not only create a structural cytoskeleton which gives some rigidity and solidity to the cell, but create the pathways along which molecules are moved to the periphery of the cell to position organelles and other structures.  The centrosome replicates during the whole cell's replication, but it replicates separately from the DNA.  Also, although the microtubules are made of tubular, a protein manufactured by DNA, their positioning, at least in part, is determined  by the location of  target protein molecules embedded in the cell membrane.  These target protein molecules are also manufactured from DNA recipes, but their position in the membrane, a position which effects the entire movement of materials during the cell's growth process, is not determined by DNA.  The way that target protein molecules are positioned is not known, but it seems to have something to do with their alignment with the protein molecules embedded in the membranes of adjacent cells.  Also embedded in the cell membrane are sugar molecules which  embed at various angles to the surface of the membrane and at various positions on the 
membrane.  It is suspected that there is a 'sugar code,'  possibly more complex than the genetic code, which determines the spacing and relationships between cells.

What the structuralists had hoped to find were laws of form that would explain the basic morphologies of the world of living organisms and would account for the course of evolution.  To find a law, or set of laws, that would make orderly and legalistic sense of the myriad shapes of living creatures, from microscopic to gigantic, from almost four billion years ago to today, including all plants, all animals, all fish, all birds, reptiles and insects, seems, by the enormity of its scope, to be doomed to failure.  Also, it is obvious, no matter what position one holds, that living creatures are adaptive.  In fact you can make a case that the bulk of living behavior is adaptive, as living creatures attempt to get what they want from a constantly changing environment.  Although there are biological processes, some of which I mentioned above, that are not affected by environmental factors and do not change over time, certainly the shapes of bodies, and of internal biological systems, are responsve to environmental demands, whether that response is accomplished in a Darwinian manner, or not.  The avian feather has a masterly design for a flying creature, as has the avian lung which, unlike any other lung, takes in and eliminates air continuously and simultaneously.  Whether these features, both of which make a sudden appearance, fully formed, in the fossil record, without any clear antecedents, were a result of a Darwinian process of evolution or some other process, it is hard to imagine that they resulted from a process that is immanent in the materials of feathers and avian lungs, and that did not somehow take a flying environment into account.

The failure of the structuralists to find such a set of laws was what opened the door for the acceptance of Darwinian functionalist thought in the second half of the nineteenth century.  The Darwinians, in turn, had hoped to discover the genetic blueprint in the genes that would specify or determine the actual form of the organism.  Yet this search has also failed.  In fact there does not seem to be any relationship, not only any proven relationship, but any conceivable relationship,  between genes and shapes.  In complex multi-celled creatures each gene, with few exceptions, is used in the construction and maintenance of several different parts of the body and is involved in many different shapes.  To try to find a process whereby living forms are shaped through a genetic method or through a legalistic method both seem equally doomed, which they have been, in spite of decades of research whose aim has been to find just that.  Is there yet another possible way of looking at this whole problem that promises to be more fruitful?
           
                                     A THIRD WAY

Beyond structuralism and functionalism, there is a third position in this argument, but the people that hold this position are usually not scientists and they usually don't argue.  The fact that I hold this position and, although I am not a scientist,  have a strong interest in science, and that I am argumentative as well, may be an anomaly. Yet, whatever it is, and for whatever it's worth, here follows the best scientific argument that I can muster for the  shaping of living bodies through this third way.

I have to begin not with bodies, but with forces.  The mystical (or traditional Eastern or pre-industrial) understanding of forces was and is very different than the modern Western understanding of forces.  Westerners think that the source of forces is matter, either little particles of matter or huge amalgamations of matter, and that forces move between particles and amalgamations of matter. So electro-magnetism in the West is a by product of the positive charge of a proton and the negative charge of an electron.  Electro-magnetic positivity and negativity radiate from and between positively charged or negatively charge particles and they result from immanent qualities of those particles.  The same is true for gravity.  Gravity is a force that extends from a larger body to a smaller body and back.  Gravity is a force between physical bodies and is a quality of the mass, the sheer amount of physical stuff,  in those bodies.  And the strong and weak forces of Western physics are the by product of attractions between sub-atomic particles.  

As strange as it may seem to Western ears, the mystic idea of forces is that they do not emanate from matter; that matter, in fact, or the illusion of matter and solidity, comes from the attraction between forces; and that forces, rather than emanating from and toward matter, actually attract each other and form configurations, including stable configurations, made up of just mutually attractive forces.  It is the fields of force created by these attractions that create the experience of impermeability and solidity rather than any emanations from particles.  In fact there are no particles.  Seeming particles are more condensed associations of opposing forces within a larger context of opposing forces, like whirlpools in a stormy sea,  or tornadoes in a windy sky. 

The two opposing forces of which mystics and pre-industrialists and traditional Easterners speak are called, variously, yin and yang, in and yo, Tawa and Takpella, Heaven and Earth, Shiva and Shakti, celestial and terrestrial, Mother Earth and Father Sky, etc. One is an expanding, centrifugal force and one is a contracting, centripedal force. I have spoken a lot about these forces in other posts:  how they behave, and how an understanding of them transforms one's perception of the world.  What we call solid objects, including stars and galaxies of stars, and planets and organisms and cells within organisms and molecules and atoms and subatomic particles,  are all yin and yang in combination and combinations of yin  and yang within combinations of yin and yang.  The appearance of solidity is caused by the stability of these forces keeping each other in balance.

At the center of each naturally formed object is pure yang.  Man made objects are not necessarily more yang at their center, although they include a multitude of atoms and molecules which are, themselves, more yang at their center. This pure yang center is held in place and prevented from going where it really wants to go, which is to the closest strong yang (which, on earth, would be the center of our planet) by the outward pull of yin, which, in turn, is held in place by the inward force of yang and kept from going where it wants to go, which is to expand out and disperse through the universe at infinite speed.  Without yin, the yang center of any earth bound object would quickly collapse into the center of the earth, which would quickly collapse into the center of the sun, which would quickly collapse into the center of the Milky Way Galaxy, which would quickly collapse, along with every other galaxy, into the yang center of the universe, which is located at the non-physical center of the expanding 'balloon' of the world of 'matter' (actually the world of yin and yang in combination).  Then we would quickly be back to exactly where we were at the time of the bifurcation of yin and yang, when the universe first began.

While pure yang exists only at the very center of natural objects, pure yin expands at infinite speed throughout the entire universe.  It is found wherever yin and yang in combination don't already exist.  In other words, pure yin is everywhere the material world is not, including all the interstices between combinations of yin and yang.  Wherever there is unbound pure yang, it is instantly 'captured,' surrounded and held in place, by pure yin.  This sudden appearance of yin formations the moment there is unbound yang, is the 'proof' that scientists discovered for the existence of a Higgs boson and a Higgs field that captured all the news a couple of years ago at the CERN particle accelerator in Switzerland. 

In other posts I talk about how many of the mysteries of modern physics are explained much more simply through an understanding of yin and yang.  Please look at the following posts: 'Particle Fever,' 'Yin, Yang and Beyong,'  'The Complete Theory of Nothing,' and Understanding the Quantum.'  My point, in this post, is that a charged pattern of forces, a configuration of yin and yang energy,  precedes the physical body, and as the embryonic cells grow, expand and differentiate, they migrate  to fill out the patterns of positive and negative energy that are already there.

This may seem like a very far out perspective than the two that are currently held by the scientific community, but I remind you that  the functionalist position offers only mutations as a means of change, and there are no known genetic mutations that, by themselves, create any improvement in shapes; while the structuralist position posits a set of laws, without discussing the origin of those laws, which determine underlying shapes, but no explanation for an evolutionary method of change other than to say that it is adaptive.  

Although it may seem far out to you, yin and yang is the basis for acupuncture, moxabustion, shiatsu massage and aryuvedic medicine; in fact it is the basis of all traditional Eastern therapies and of traditional, pre-industrial, therapies here in the West.  Of course you may think that these traditional therapies have no real medicinal effect and if they result in any improvements at all it is because of the placebo effect that comes from uninformed people holding primitive beliefs in their efficacy.  Chinese veterinarians commonly use acupuncture to sedate pets during operations.  It is hard to think that the sedative effect of acupuncture needles in this case is due to the irrational beliefs in their efficacy held by Fido and Mittens.  The therapeutic effects of acupuncture are so widely accepted that even Western health insurance companies, those most conservative of institutions, have been forced to insure acupuncture treatments for many painful ailments.

In acupuncture, needles are applied along spirallic meridians that transect the body.  These meridians are not just the arbitrary result of how material organisms happened to form, but are the energy structure that precedes the physical body and that the cells of the physical body organize themselves around.  (Cells, too, are themselves configurations of energy, within the larger energy configurations of organs, tissues and the energy configuration of the entire organism, but I will continue to refer to them as if they were solid physical objects.)

Energy, as it operates in organisms is considered to be,  in the West, positively charged and negatively charged particles repelling and attracting each other.  Positive charges correspond with yang and negative charges correspond with yin, with the following caveats:  Yin and yang are not qualities of matter, but create, themselves,  the illusion of matter.  Positive and negative refer, usually, to the slight imbalance of much more yin/yang forces within the object, which go undetected because those two much greater opposing forces neutralize each other.  That is why, when atoms are split, enormous forces are released.  These forces are the same as the positive and negative forces that we detect in stable atoms, it's just that that stability is caused by much stronger amounts of yin and yang held in balance.  Also, while yin, or negativity, captures any unbound yang, it is not really drawn to it. Pure yin expands endlessly and is everywhere that matter is not.  It is not drawn to unbound yang; it is already there.  The two forces capture each other, bind each other, but are not 'drawn' to each other.  They, in fact, pull away from each other and it is this tug of war, this bound field of opposing forces, that create the illusion of solidity and the relative permanence of form.  What is drawn to each other, what could be more accurately described as an attraction,  is between amalgamations of pure yang with larger amalgamations of pure yang.  The attraction between amalgamations of pure yang at the center of naturally formed objects is what we call gravity.  

                 YIN/YANG AT WORK IN ORGANISMS

Many, if not all, intracellular processes depend on the lightning speed locking of certain kinds of molecules with others.  How protein molecules and Rna molecules lock into nucleotides and into mRna polymerase was once described to me, by a molecular biologist, as a molecule trying on each nucleotide as if it were trying on a jacket to see if it fits; and this at the rate of a thousand jackets per second.  He, of course, knew the rate at which this process  took place but had never actually witnessed these one thousandth of a second attempts by molecules to see if they fit into each other.  The same is true for the lightning speed in which tRna molecules and amino acid molecules come together and how the other side of the tRna molecule is matched up and fitted to the 'tape' of mRna molecules being fed into a ribosome, and the speed at which the right binding sites of antibodies bind with the compatible surfaces of antigens.  It's hard to imagine all of this taking place at lightning speed if each interaction requires an actual physical encounter to see if there is a molecular fit.  Keeping in mind that molecules and atoms are not solid encapsulated objects, but opposing forces in a stable configuration, then these 'fittings' are more understandable.  The pattern of positive and negative energies at the periphery of the molecule, or at it's binding site, attracts the passing molecule or antigen to it.  In other words, there is no actual physical 'fittings' or trying on of molecules.  The process happens at some distance, even if the distance is tiny.  If there is no compatibility of the two energy patterns, then the unbound protein molecule or nucleotide or antigen just keeps moving, being repelled by this incompatibility, and being pulled in and bound by the one molecule or binding site where there is perfect compatibility.  This attraction at a slight distance, and gliding by if there is no compatibility,  makes it much more conceivable that a protein molecule could 'scan' a thousand nucleotide bases every second rather than a physical object "trying on" a thousand other physical objects every second.  

Much has been discovered about the direction of the movement  of materials within a cell.  Organic material needed for intracellular construction, even entire organelles,  are dragged along microtubules by dynein motor molecules that move material to the plus end, toward the periphery of the cell, while  kinesin motor molecules  move waste construction material back to lysosomes at the minus end of a microtubule,  toward the centrosome adjacent to the nucleus, where they are broken down into reusable material.  (Google 'dynein animation Harvard' to see amazing animations of these motor proteins at work!).  This aligns perfectly with an understanding of yin and yang as I explain in those other posts.  Yang is centripetal and contractive,  so it pulls yin in toward the center.  The boundary of any configuration is made by yang restraining the expansive force of yin.  A cell, like all objects, both organic and inorganic, that are formed by natural processes (but not man made processes), would be more positively charged (yang) at their center and more negatively charged (yin) at their periphery.  The minus, yin end of the microtubule attached to the positive, yang force at the centrosome, and the positive, yang end of the microtubule attaches to the negative, yin forces at the periphery.  In this way more yang objects, that would naturally migrate inward, are dragged outward where they bind with more yin elements and are held in place toward the periphery, while more yin waste products are moved back to the yang center where they are broken down in lysosomes.  This is how centers of activity, organelles with yang centers, find stable locations throughout the cytoplasm and a more complex, eukaryote cell is formed.  This is in contrast to  prokaryote cells, which do not have these microtubule structures, and where all the yang material gravitates toward the nucleus and all the yin material is dispersed throughout the cytoplasm.  

Also, the manufacture of structures that append outward from the surface of the cell wall have been well studied.  These are the cilium and the flagellum.  I will not discuss the complexity of the cilium or the stunning complexity of the flagellum, which appends to 'simple' bacteria, but I suggest you look at that elsewhere, especially in the works of Michael Behe.  Interestingly, both appendages are constructed around a microtubule, but a microtubule which is aligned with the negative end at the cell surface and the positive end appending outward from there.  What negative cluster of energy is that microtubule attaching to that allows it to be a rigid girder along which construction materials can be transported outward, when it is not attached to matter within the cell, but is attached somehow to the space surrounding the cell?    Why do the dynein motors stop walking material out at a certain point and then kinesin motors start moving excess material down the microtubule and back toward the cell?  Why this switch from dynein to kinesin takes place is not known, but this is the very thing that is creating the length of the cilium and the flagellum, a length which is very precise, because the cilium and flagellum can only work effectively if their length is in the proper proportion to the size of the cell.  Doesn't all of this strongly suggest that there is a negative energy, a yin concentration in the space surrounding the cell, a concentration that could only happen if there was a spot of pure yang to which the yin was attracted, and that the positive end of the microtubules are binding at that cluster of negative energy and the dynein motors which always walk material toward the spot where the positive end of the microtubule attaches, stop there, and kinesin motors, which always walk material away from the positive end, then take over and start doing exactly that?

                        FORCE FIRST CONSTRUCTION

When a building is built it is necessary to have a plan.  The more complicated the building, the more intricate and precise the plan must be.  Of course there is no human construction that rivals in complexity a living organism.  Even a bacterium, the single celled creatures that began life almost four billion years ago, has a molecular complexity far beyond the complexity of any human construction.  That is why there are burgeoning microbiology departments in prestigious universities all over the world, and the leading lights of these departments are winning Nobel prizes every year.  The four billion year old cell, one millionth of the size of the head of a pin, is still, after all this study by some of the brightest people on this planet, full of mystery.  We are merely scratching the surface in our understanding of single celled organisms.  

A building plan, or blue print, shows in detail  the shapes and shapes within shapes that the architect wishes to achieve.  The prospective owner of this building sees in the blue print the shape that his building will take.  The builder of the building, however, sees in the blue print the plan from which he or she can deduce which forces to use to assemble the materials of the building, and how much force and when to apply it.  The building is actually constructed first from an idea which materializes into a written plan, then a construction idea, which is a planned use of forces, and then the actual construction takes place.  A plan of how and where and when and with what intensities to apply force always precedes the actual construction.  

During the construction of living organisms. three processes are occurring simultaneously.  One is the mitotic division of cells, so that one fertilized ovum is transformed not only into the two trillion celled body of the new born, but into the placenta, the amniotic sac, and all the temporary organs and organelles that the baby needs before he or she is independently able to circulate blood, eliminate waste and digest food. A second process is the differentiation of cells, so that, in the case of humans the ovum, is transformed into  two thousand different types of cells, in the exact right amount of each.  The third process is the migration of cells so that, somehow, the right combinations of these two thousand different types of cells migrate into the exact positions that they need to be in to create working systems and organs of various types.  

Much has been discovered in recent years concerning the methods by which embryonic cells migrate during gestation.  Many of the mechanisms by which a cell moves are now understood.  What is not understood is what determines why a  cell migrates in a particular direction. It is like knowing that a steering wheel is connected to a steering column which is connected to an axle and, in turn, the axle is connected to wheels that are connected to tires.  So we know that turning the steering wheel changes the direction of the car.   What we don't know is who is steering.  

What is now known regarding cell migration is that before it can commence,  polarity must be established.  Let me repeat that, because it is so important.  Before cell migration can commence, polarity must be established.  Polarity means that through the migration of intracellular material, positively charged materials are moved to one end of the cell and negatively charged materials are moved to the other end.  One side is now the leading edge which expands forward by actin filaments and microtubules stretching the cellular membrane forward at the leading edge, and filaments and microtubules contracting the cellular membrane and pulling it up at the rear end.  Thus embryonic cells crawl there way slowly through the viscous environment of the uterus.

The movement of the cell is a continuation of the polarization of the cell.  The whole cell continues to move in the same direction that the charged material within the cell moved toward the leading edge.  What could possibly cause this polarization but a source of energy external to the cell, a positive source drawing the negatively charge particles to it, or a negative source drawing the positively charged particles to it?  And remember, the orientation that the cell is in after it is polarized, the angle of the front end to the rear end is the direction that the cell will continue in until that next level of embryological development is reached.  What else could create this precise polarization of cells but an equally precise  structure of positive and negative energies, of yin and yang, that pre-exists any physical structure? 

Where did this energy body, or force configuration, come from?  It certainly wasn't there in the woman's body before conception.  The shape of this energy configuration reflects the genetic features that are contained in the fertilized ovum, so it had to emerge co-incident with the fertilization or shortly after fertilization.  And it must have an intertwined relationship with the genetic make-up of the cells of the growing embryo.  Somehow the genes of the newly fertilized ovum are like receivers that attract this energy pattern to them, and the energy pattern reflects both the primal shape patterns that make that species unique among other species, and the specific adaptational shapes that make that one individual fetus  unique among the other members of that particular species.  

It is wondrous, isn't it?  But the process itself is wondrous.  How else to explain a wondrous process of a fertilized ovum forming into a unique shape that is indicative of its species, except by a wondrous explanation.  Certainly the genes within the individual cell cannot polarize, by themselves, the materials within the cell; and all the thousands or millions of cells that are being polarized in precise specific migrational directions could not achieve that remarkably specific, synchronized alignment by themselves.  They must be responding to a pattern of energy that is larger than the entire cell mass of the embryo and is causing that mass, as it expands, to be drawn in all these slightly different directions toward it.  And there certainly is no law that could be found that would make it inevitable that this shape would be formed by the inherent chemical qualities of the components of the fetus unfolding in an undifferentiated lawful way.  Since each fetus is unique, there would have to be a unique law for each situation, which is to say, that there is no law, because the purpose of a law is to give uniformity to behavior.  Here we would have to have a different set of laws for each species and a different set of unique exceptions to that law for each individual member of that species.  So neither structuralism nor functionalism will help us here. 

As I have said, I am not a scientist.  I have no laboratory facilities, nor the know how to test my ideas as hypotheses.  I believe they are testable, that energy patterns surrounding the growing embryo could be found, but not by me.   Just like at CERN where there were theoretical physicists waiting for engineering physicists to test their theories; the proof for  this theory would have to wait until experimental biologists had the interest and could find the courageous financial backing to conduct such experiments (courageous because in our current scientific zeitgeist it is always an act of courage and professional risk to try to do any experiment that could wind up with a result that would be contrary or even challenging to neo-Darwinian dogma).

            CONSTRUCTING AN ENERGY PATTERN

The structuralists believed that the primal patterns of nature originated in the mind of God.  If, as the monistic dualists think, one becomes two and then becomes the multitude that we see, then God's will or the will of the Infinite is manifest through yin and yang.  This section is an attempt to shed some light on how that process could work.

Keeping in mind that the material world is made up of yin and yang in combination, so no thing and no one is purely yin or purely yang, here are some descriptions of what it is like to experience both yin and yang.  In terms of desire, yin is the desire to lose oneself in another, in a group, in an activity.  It is a desire to expand beyond oneself, to commune with nature, to love, to lose oneself to a cause or to an activity, to be an indistinguishable part of an ensemble, a team, an orchestra, and, spiritually, to disappear, like a drop of water into the ocean of the Divine.  Yang is will, concentration, the desire to distinguish oneself, to stand out, to make a unique contribution, to be remembered, respected, individually appreciated and acknowledged.  It is the desire to forge ahead, to carry through with a plan or an objective, to succeed.  So, while yang strives to solidify Self, yin strives to obliterate Self, to melt the boundaries of Self and Other.  

As I said before, yin and yang are the names that I am using, but they refer to the same opposing forces that are referred to in all pre-industrial cultures.  Here is some language from Coleman Barks, 'The Soul of Rumi,' speaking of fana, which is the Arabic equivalent of yin, and baqa, which is the Arabic equivalent of yang.  

"Fana is the streaming that moves from the human out into mystery-the annihilation, the orgasmic expansion, the dissolving swoon into the all.....Fana is what opens our wings, what makes boredom and hurt disappear....We are the dreamer streaming into the loving nowhere of night. 
Baqa means 'a living within.'...Life lived with clarity and reason, the turning again toward what somehow always was.  The concentration of a night of stars into one needle's eye....The absorbing work of the day.  The precise painting of a piece of trim...a return from expansion into each's unique individuation work."

As with everything else in the physical universe, the building of cities is the result of the interplay of yin and yang.  You have heard the expression, "Build it and they will come."  This is not always true.  First off, many who are familiar with that phrase have never built anything.  To build something, to create something new, to invest time and energy into something where there is no proof of success, requires will and vision, daring and persistence.  Also, sometimes something is built and no one comes.  The building, whatever the hopes for it initially were, never succeeded in attracting the people or the activities necessary for it to succeed.  But those people who do build it, and have the vision and depth of understanding of what people really want or need, and the persistence to stay with it and insure that when people come they will be treated in such a way so that they will return, these people do succeed.  They succeed to the point that so many people are attracted to that building, or outpost, or factory, that soon other establishments are built around to support the original one.  These establishments also require will and vision and courage, but, perhaps, not as much as that of the builder of that first establishment.  These others are building into a known market.  The people are already there; the need already exists, or can be more comfortably calculated.  

At a certain point, this conglomeration of buildings and people, first initiated by one person's vision, gets congested to the point that some one else, another visionary, has the idea of building another center, another structure to which people will be attracted, at some distance from the original hub.  The initial construction of a peripheral structure also requires great courage, vision and persistence.  It is also a striking out into the unknown.  And when this is accomplished successfully, then the city now has another center of attraction, another spot where houses and shops and schools and roads and infrastructure will spring up.  And this same process is repeated over and over again as large, complex metropolitan centers develop.  But notice, at each initial step, the initiation of the city as a whole and the initiation of peripheral centers, great courage, vision and will are required.

People that start and successfully carry through with such daring projects are often referred to as having a 'fire in the belly.'  Everyone knows what that means.  It is not a literal fire that anyone else can observe, but it is the powerful will, the drive, that is experienced as a heat or a contraction, or both, in the center of the body, the belly.  This is the experience of yang.  We all have yang, but to have a strong and deep yang center, to have a dream that stays with you until it is fulfilled, that burns at you, this burning is yang and is experienced at your body's center, the belly.  And notice, if the yang is strong enough, is deep and persistent, then whatever is needed, the yin elements, will be attracted to it.  

The easier thing to do, is to join what is already in place; to move to where the action is.  There is nothing wrong with that and we all do it at different times.  But if you have a dream, if you are starting something new, something for which there is not an already established market or demand, that requires a strong and deep yang force, a fire in the belly.  Once the true visionary makes the move, then the assistants, the constructors, the consumers and everything and everyone else will follow.  

It is the same thing with natural construction.  The movement of yang is toward the center.  To get yang away from the center requires effort.  Within the cell powerful dynein motor molecules move whole organelles with yang centers away from the center of the cell toward the periphery where they are bounded by yin elements which hold this new peripheral object in place.  It always, in natural or human construction, requires will and energy to move or create a new object (or a new center of yang attraction), with the capacity to 'capture' or attract other objects, away from the original center and out to the periphery. 

Now when we humans do things, and I am not talking now about courageous constructions, but everything that we do, from getting out of bed in the morning, to brushing our teeth, to getting a Nobel Prize or constructing a palace; all of these begin with a desire, an intention to accomplish that particular thing or activity.  And that desire is preceded by a restlessness, an imbalance of energy, that forms into, or semi-materializes into, a specific desire, whether the object of that desire is visualized or not (as I said earlier, if the desire is to accomplish, or construct, something very complex, a detailed visualization of a plan, if not some kind of written plan, will be required).  What sets everything in motion is yang.  It doesn't take a powerful yang, a fire in the belly, to get yourself a glass of water, but if you are sitting down, it takes enough yang to overcome the inertia of not getting the water and just sitting there.  In fact, if we are feeling really tired or lazy, if we are in a very yin state, where we are just completely passive and inert with circular thoughts rather than directional thoughts, we may just continue to sit there longer until our thirst becomes strong enough to make the sitting intolerable.

Each of these activities, even the simplest ones, requires a translation from intention (yang) to whole cascades of millions of neurons leading to muscle cells and millions of molecular reactions within those muscle cells to allow us to do what it is that we intend to do.  How is this accomplished?  Although it is taken for granted that living things automatically do what it is that they want to do, this translation of desire to action is utterly mysterious.  The best I can say is that the energy of intention (yang) charges the initiating neurons that begin this process.  The way that the particular pattern of initiating charges is selected among the two hundred billion neurons of your brain, and the way that the particular path leading from the initiating neurons to specific muscle cells and molecular reactions within those cells is accomplished is another great mystery, but it seems to me that there is no other conclusion than that having a particular body and brain is a way of being able to live out, to experience the satisfaction of, fulfilling a particular set of intentions within a particular environmental niche.  

If we are able, simply by intending it, to initiate the firing of patterns of millions of neurons, and do that at every waking moment of our existence; then, I think, that the Infinite, the Cosmic Consciousness, is able to create yang centers of energy, away from the central yang of the universe, simply by His/Her focus.  Yang is the focus of the Infinite.  The most intricate patterns of energy are created by the Infinite focussing on certain spots with different intensities and angles.  As I said, yin is everywhere.  Yin is immediately captured by this yang, and a spiral is formed with yang at the vortex of this spiral. 

The physical universe consists of spirals within spirals, from the tiniest yin/yang spirals of quarks and other seemingly subatomic 'particles,' to the spiral arms of galaxies containing billions of huge seeming 'particles' called stars, to the largest spiral of all, which is the spiral of the entire world of matter spiralling around the non-physical yang center of the universe.    

Organisms are intersecting spirals of yin/yang, and the vortex of these spirals is always yang.  These yin/yang spirals can be circular, but not a perfect circle, or  linear, but not a perfectly straight line, or it can be anything in between. Also, there is always a space between the yang vortex and the spiralling yin part, because yin and yang are not attracting each other, but are capturing each other.  The yin is pulling away and the yang is contracting in. 

We are born in a fetal position, which is a spiral.  Our legs, moving from the hips to the feet are in a spiral position, as are our arms, from the shoulders to the hands.  Toe prints and finger prints are, also, both spirallic patterns.  The digestive system, with the espophagus ending in the coil of the intestines,  the nervous system with the spinal cord ending in the brain, all these are spirallic formations.  And there are spirals within spirals, within spirals.  The atom, itself, contains many tight yin/yang spirals that we refer to as subatomic particles, although we have never seen these particles, and have no idea of how they could be made of any solid thing.  All we know about these particles is their mass (the amount of yang inward pull on the spiral), their spin (whether it is spiralling in a clockwise or counterclockwise direction) and their charge (whether the amount of yin and yang balance each other, or whether there is more yang, positive, or more yin, negative). 

These spirallic forms of energy polarize cells and draw them to them.  They set the contours of all the shapes of the body, and shapes within shapes.  They electro-magnetically align protein and sugar molecules embedded in the outer cell membrane so that cells are aligned to work in perfect coordination with each other.

We are intertwined and intersected by the Divine.  We live out a particular life experienced through a particular organism.  We choose this limited, separated, focussed experience.  The quality and shape of the particular organism that we are in, which is formed by the yin/yang energy configuration and the particular genome that corresponds to that energy formation, is one that you could say that we choose, or that the Divine chooses for us; but since we are so intertwined, since we come from the Divine, are part of the Divine, and return to the Divine, we can say that the particular genome, the particular shape and the particular social and cultural circumstances of our birth are all things that we (before we were separated into different organisms) chose for ourselves.

Just as with humans, the amount of yang force that we have results in how much we are able to accomplish, by willing things to happen and having the persistence and courage and force of attraction to bring all the elements necessary together to accomplish our goal; so it is with the Cosmic Consciousness, that by willing a pattern of yang centers of focus, all the yin elements are attracted to it to create all the spirallic forms that fill the natural universe.  What biologists study are the mechanisms whereby the materials of construction are selected and moved into place, the timing of gene expression, the manufacturing of proteins from gene recipes and the distribution of proteins throughout the growing organism.  What is not studied is how the precise directions that these materials move to is determined so that they result in recognizable and functional traits and organisms of specific species and how these shaping mechanisms first originated. 

I have presented my ideas about how such things take place.  If you think differently or have any comments about what I have presented,  please let me hear from you.

Peace! 
















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