Life Inside the Cell: Waking Up to the Miracle, part 1

Understanding the New Phylogeny of Angiosperms, part 1

[This is the first in a series of three posts, this one on life within the cell, the second, on the evolution of plants, and the third on the New Phylogeny and Eudicots.  While trying to understand the later, I found it necessary to better understand the others, what was behind this reorganization of how we look at plants.  To do that requires going back in time and scale to see what we are really taking about when we consider plants and the life within them.]

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I begin here with the cell.  I will not spend time discussing its structure and various parts, the differences between those of plants, animals, fungi and bacteria.  That has been done by many others, elsewhere.  Instead I want to present here what I’ve learned about what makes the cell, its existence and life within it, so amazing, something that which should give us all pause, when we consider our own lives and what we do.  When scientists ‘split hairs’ in their arguments on which group to assign a species, when they attempt to link them to their ancestors, many of which are now long extinct, to understand their relationships with other organisms, they have a purpose.  They are looking much deeper into what a plant is, what constitutes life and how it evolved.  Phylogeny, the science that attempts to establish relationships between different organisms, different species, to link one to the other across time, is about both the history and the continuing journey of life on this planet.  It promises to tell us much about our own place as well as that of the hundred’s of thousands of other species with which we share it.  Ultimately, if we choose to understand this, it will change the way we garden and our relationship with the many landscapes that cover the Earth.  Our gardens are our own personal expressions, works of ‘art’, and must live within the parameters of life in effect on our little pieces of ground and the Earth.  They reflect our understanding of the limits and possibilities at work here.  The better that we understand this the ‘better’ our gardens will be, the more in synch they will be with life.  

Life Inside the Cell: On Being Alive

Life on Earth is nothing without the essential processes of photosynthesis and the metabolic ‘pathways’ that have evolved within organisms that enable, support and define it.  The cell, its apparent simplicity of structure, is in reality a  complex and incredibly well coordinated organic structure, animated and defined by its internal processes.  The cell is the most critical development in the long evolution of life.  It is basic to all organisms, including the largest multicellular ones, like the Blue Whale, the Giant Sequoia, sprawling clonal individuals of Quaking Aspen and fungi that spread over many acres of landscape.  Respiration, the capacity to form proteins and the enzymes and catalysts that trigger, signal and help coordinate an organism’s many functions, DNA, their ‘plan’ and ‘instructions’, the code within every organism…are essential  ‘pieces’ of the cell.  Their basic cellular requirements have been evolving for billions of years and are continuing to do so.

It is through photosynthesis, the splitting of the water molecule in the process of harvesting energy captured from the sun, something we are told about as children, though it is a considerably more complex process than the simple ‘magics’ that were used to describe it to us then, that the world is transformed.  The interaction of the sun, water and the cell are the basis for organic life.  Life on Earth is solar powered and the water molecule is an essential element to it.   The process of photosynthesis is, on its surface, a simple and elegant process unique to plants.  While plants, like animals, consume energy to metabolize and grow, plants also harvest and transform the sun’s energy to build the basic compounds which they require to live, including energy rich carbohydrates and the little energy packets that they are converted into, ATP.  Animal life, relies more on the consumption of the nutrients, carbohydrates, fats and many of the compounds, proteins and amino acids, created within the cells of plants later consumed by animals.  Animals are capable of metabolizing many enzymes, catalysts and compounds that they require, but they still must consume the proteins and many rudimentary building blocks which these are built of, from other sources, plants and animals.  Animals are, however, capable of absorbing, utilizing, some of energy directly from their environment to help maintain their critical systems, both light and heat energy, in a way similar as do plants.  (Here is a link to an earlier blog posting I made on the three different photosynthetic pathways: the original C3, C4 which developed with aridity and predominates in drylands grasses and CAM which is best adapted and common in plants from hotter arid/desert areas.  Scroll down to the subhead titled: ‘Water and Photosynthesis’.)

Organisms are the ‘products of a ‘living’ process, the progeny of their parents, reproduced and reproducible, whether fixed in place or mobile, dynamic and coherent internally, very much more than a collection of parts.  As a western civilization we have a tendency to think in mechanistic terms even when considering life, as if it were only a different type of machine, reproducible on an assembly line, energized and maintained like any other mechanism we might build.  But that is us projecting our ideas upon the world.  Life, in a sense, has developed its own recipe, with its precise content and proportions, energized by the very process of its creation, to stimulate particular internal chemical reactions that in this case spark a self organizing and ongoing process, resulting in ‘organisms’ with particular and shared architectures at every scale, organelles, cells, tissues and an overall organizing structure, proven over time, recorded in one’s genetics, complete with ‘operating instructions’ to metabolize, respire and reproduce.  The metabolism and respiration of living organisms, in turn, contribute to the same conditions an organism requires for life, helps them maintain themselves in an energized state of ‘disequilibrium’ without which an organism dies…and they have a likewise effect upon the environment in which they live.

Plants are most definitely ‘alive’.  Each exists, energized, in an ideal state, of dynamic ‘disequilibrium’.  Death is an equilibrium state, the energized ‘structure’ of the organism, neutralized.  The energized relationship between each and every part, absent..  Stasis.  Plants live within a narrow range of ambient temperatures, of heat.  Below this and they begin to shut down. their metabolism and respiration unable to continue.  In the case of temperate and other plants from cold regions, they can suspend these functions in a state of dormancy, when temperatures drop below their threshold, while holding themselves in a kind of ‘tension’ that increasing temperatures will ‘kickstart’, again in to ‘motion’ when temperatures warm sufficiently.  Energy is contained within their living structures as part of their very being.  Organisms are not some kind of organic equivalent of the classic heat engine.

In a mechanical heat engine fuel is burned, heat is produced, and its energy is captured typically by a spinning turbine or by pushing a piston, that is then converted into mechanical energy and can accomplish ‘work’.  This can only happen when the ‘used’ heat, its work potential captured, can then be exhausted into a cooler space and the cycle begun again.  If temperatures on the exhaust side are equal to the ‘input’ side, no work can be accomplished…such an engine is in an equilibrium state.  Under normal operation the exhaust will gradually heat both the ‘mechanism’ and the surrounding ambient air reducing the engine’s effectiveness as the difference between them diminishes.  This does not happen in an organism, plant or animal.

Organisms operate internally in a state of disequilibrium as if continuously perched on the edge of action, requiring only the slightest ‘push’ to move them.  Their structures themselves contain an animating energy.  To do this requires that they remain within specific operational parameters or limits.  Organisms are capable of utilizing the energy available to them directly through ambient conditions, that both warm and charge them via specific wavelengths of electromagnetic energy, visible light and the infrared gained by heat. They are dependent upon the ambient temperatures that surround them.  As these move much above 90ºF or below 40ºF the species capable of long thriving begin to rapidly diminish, unless they have devised strategies to ‘bridge’ these periods.  The ambient conditions, along with their own metabolism, create the necessary energies for their individual lives.  As long as their other needs for water and various nutrients are met, they will likely continue living.

Plants require minimum levels of CO2 for photosynthesis and of O2 for respiration.  Green plants photosynthesize producing energy rich compounds, carbohydrates, that they use to metabolize while producing various, compounds, proteins, enzymes and catalysts  within their organelles from the soluble nutrients available to them in surrounding water, dissolved, diffused into it from the adjacent soil.  Utilizing the energy held within the chemical bonds of these carbohydrates, plant cells, produce the energy rich molecule, ATP, which contain essential electrical charges within its bonds that power the cell.  Plants do not ‘burn’ carbohydrates anymore than do we within our cells, oxidizing them, to produce heat as they do in a combustion engine.  If we did we would ‘burn’ up our own tissues as a result of the heat required to power our systems.  While birds and mammals do produce body heat as warm blooded animals, plants, fish, insects and the many microscopic forms of life here, do not.  Our warm blooded capacity is the result of an innovation, one that separates us from other life in that we are able to produce at least some portion of our own heat to maintain an optimal working temperature within our bodies, just as we have developed a variety of strategyies to ‘waste’ excess heat and cool ourselves when needed, unconsciously.  So called cold-blooded animals and plants don’t do this.  They are completely dependent upon the ambient temperature within which they live.  Warm blooded organisms are more complex, later developments along the evolutionary path, that require more calories to maintain their internal conditions.  Like us, each organism has an optimum temperature range and all of them lie within a relatively narrow window related to the temperatures here on Earth and the physics of the unique molecule that is water.

Every chemist knows that chemical reactions are temperature dependent.  As temperatures warm, reactions accelerate.  Too cold and they stop, too hot and they rage out of control.  This is true within organisms as well as in test tubes in a lab with the added caveat that significantly too high can result in the breakdown of the enzymes and proteins necessary for life.  They also understand that chemical reactions, wherever they occur, are ‘electrical’ in nature.  Reactions may yield heat or absorb it, but the connections within the molecule are electrical..Molecules and compounds are held together by electrical bonds.  To transform a compound either requires an energy input that ‘breaks’ these bonds and results in a release of energy, or uses this added energy to form ‘new’ molecules that incorporate this energy in their structures.  This process is dependent upon the nature of the  compound and its bonds.  Carbohydrates are held by energy rich bonds.  (Remember your high school chemistry?)

C6 H12 O6 + 6O2 <=> 6CO2 + 6H2 O

(1 simple carbohydrate + 6 oxygen molecules <=> 6 carbon dioxide + 6 water molecules)

<< sun light – energy >>
<< photosynthesis – respiration >>

 

Moving left to right this is the equation for respiration, whether in a plant or an animal…the oxidation of carbohydrate, and releases energy for use within the cell.  It is the opposite of the reaction taking place in photosynthesis.  Photosynthesis moves right to left utilizing the converted solar energy in its bonds, ‘storing’ it.  Respiration moves left to right releasing that energy for metabolic processes within the cell.  Electrical energy.  As part of this energy conversion within the cell the mitochondria converts this into the more available form of Phosphate rich ATP which is transported around the cell and organism to power needed metabolic processes.  Essential to this is the water molecule whose capacities have shaped the functioning of an organism at every level.

Water: The Magical Ingredient

Much of the ‘magic’ of a living organism is attributable to water.  Water is a unique molecule in the known universe.  It alone is capable of the ‘phase’ changes within a temperature range supportive of organic life.  It moves from not just solid to liquid to vapor, but to a higher density liquid (some refer to this as liquid ‘crystalline’ water) chemically very different than the common ‘low’ density liquid form which is the typical ‘free’ or ‘bulk’ liquid water we are familiar with.  This more dense phase of structured water occurs when it comes in close proximity to certain ‘hydrophilic’, water ‘loving’, positively charged, surfaces.  Hydrophobic materials, are negatively charged, and repel water which can cause, for example, water droplets to form on their surfaces.  When these water loving molecules are in relatively close proximity to each other, and water is added, they form a substance we commonly recognize as gels and have unique characteristics.  This capacity is part of the water molecule’s strongly ‘dipolar’ nature, possessing both positive and negative charges, which allow it to bond to itself, the proteins that comprise much of a cell and the many charged ions that can dissolve into bulk or free water.  When water bonds to positively charged surfaces they form this fourth state of water.  The molecules align themselves electrically, actually changing the molecule’s structure to H3O2, bonding tightly to the protein and itself, excluding solutes, ions, even contaminants, creating what are being called ‘exclusion zones’.   Water in this state carries a powerful negative charge turning the cell into a kind of battery rich with these charged bonds.  This charged state contributes to an organism’s state of animated disequilibrium.  Adjacent unbounded, bulk water, carries the opposing positive charge.  Charged in this way, an organism is in a continuous state of readiness capable of actions with minimal additional inputs or forces. (Check out these two videos by Dr. Gerald Pollack on the fourth phase of water.  The first is a TED Talk, titled Water, Cells and Life a shorter version of the following, a lecture he gives of water’s role in biology.

Various ions, electrolytes, readily bond to free, low density water, and are necessary for organic life.  When water bonds with a protein, it does at least three things: it ‘hydrates’ the protein, changing the protein’s physical form, releases the ions, excluding them from this zone of higher density crystalline liquid water and creates an electrical charge.  Proteins are complex, long molecules, capable of folding in a way similar to Japanese origami when ‘dry’, then ‘expanding’ or extending many times their former size when hydrated, when bonded to water.   Proteins compose much of the cytoplasm and cytoskeletal structure within the cell.  In an organism these changes are coordinated with other proteins, allowing them to ‘perform’ physical actions within the cell, tissues and organism.  They essentially ‘communicate’ instantaneously, one catalyst initiating a cascade resulting in a coordinated action within the cell or organism, producing a charge that directly influences adjacent organelles and tissues, in a healthy, functioning structure.  The availability of another ion, positive or negative, can later trigger a return to the earlier state, the charges neutralized, and water again bonded with available ions.  The process can cycle in patterns not unlike the on and off of a binary code.  Compromise the structure or the conditions too far and the field collapses resulting in the death of the organism.

Such actions can include transporting fluids within the cell, tissues and structure of an organism, contracting and relaxing muscles, releasing enzymes and catalysts that both enable and help coordinate  ongoing reactions in the organism’s structure, aiding the cell in ‘signaling’ others.  This ability to respond to different ions, potential stressors, suggests something about the pathways cells have developed, in detecting, signaling and responding in a coordinated way in an attempt to keep the organism in dynamic balance…its state of disequilibrium.  If it works for you, think of this as a state of tension, continuously ready to shift from one state to another with very little energy loss.

When thinking about water in its fourth state it may be helpful to think of it as being bonded more densely, in a highly structured arrangement, to the water molecules next to themselves matching each of their positive and negative charges to those of an adjacent water molecule, leaving no ‘space’ for ions to bond to, resulting in a ‘cascade’ of ions…as if a light switch suddenly changed the chemical composition within the cell.  This is a very simplistic and short description of what is going on within cells continuously on the scale of nanoseconds.

These cascades can be triggered by specific tiny changes, initiated by catalysts, produced by the cell and are dependent upon the precise composition and proportion of the ions within the water, both inside and outside the cell.  This balance of ions is critical to the functioning of the cell.  When certain ions are not available, certain functions cannot progress (There is a reason why various sports drinks claim to replenish one’s depleted electrolytes).  These actions can be in response to a variety of environmental stressors resulting in an ‘appropriate’ response by the cell to the stress or stimuli.  (Simple, right?) Over the course of many millions of years relationships and functions refined and evolved in such ways that were supportive of more complex cellular and multi-cellular life, requiring that this internal communication be capable of extending beyond the individual cell, to other tissues and the organism as a whole.

Life began in Earth’s waters, for a very good reason. The bio-chemical reactions that are critical to life require water and what better a medium for this to take place in than within a body of water itself, a condition more conducive to these reactions/ communications increasing their likelihood in very simplistic organisms.  The development of the cell life was first in Earth’s waters…and it remains central to its process today having evolved structures and strategies so that organisms can carry what they need within themselves.  Terrestrial organisms still maintain essentially the same conditions within themselves as do aquatic organisms that still rely upon the water they live in..IMG_9680

Quantum Biology: The Realm of Quantum Physics in the Organism

Most of us have been taught that the life of any organism is determined by both its genetics and its environment.  The genetics provide a recipe, a script, that an organism follows during its development and over its existence.  Its development and life are mediated by the conditions in effect within its environment.  An organism’s genome determines whether an organism will be an English Sparrow, a Blue Whale or a Barrett’s Penstemon.  Environment effects the size of the organism as well as much about its health and vigor, it sets limits to the ‘recipe’, but this leaves something very important out of the equation.

Sir Issac Newton first postulated that matter, all matter which would include organisms, was distinct, that space was an empty vacuum, passive, a space where objects behave in accordance with the mechanical laws that he mathematically defined, precise and predictable.  Over the last century quantum physicists have established that these laws only apply at a gross level and that much of matter’s ‘behavior’ cannot be explained by them, that matter ‘behaves’ in ‘impossible’ ways.  Two particularly troubling capacities of matter for Newton’s physics are coherence and non-locality…related ‘objects’, in particular ‘quanta’, the impossibly small particles that make up atoms and molecules, that act in a coherent way, ‘informed’ by ‘objects’ to which they are related, and, that these objects need not even be in direct physical contact with one another, that they can be ‘non-local’ while being directly and even intimately linked.  In fact, experiments have been conducted in which such correlated objects have been many miles apart, yet there ‘behavior’ is influenced by the other.  Quantum physicists today have acknowledged that ‘space’ cannot be empty and their thinking has been coalescing around a concept of an energy ‘field’ that is everywhere throughout the universe, within which all visible matter, including organisms, exist.  Many historical cultures once acknowledged this idea describing an ‘aether’ out of which all things are created and to which they will return.  Modern science is beginning to understand the reality of this.

Living organisms possess unique organic architectures, that exist within an animating ‘energy field’.  They are individually unique while also sharing genetic patterns that define them, to greater and lesser degrees, to all other organisms. They share much.   Organisms, as quantum and molecular biologists are beginning to describe them, possess ‘quantum coherence’, in much the same way as do correlated ‘quanta’.  Each part of an organism is in intimate and direct ‘contact’, ‘communication’, with every other part.  They are precisely correlated internally as individuals and to others to progressively lesser degrees as you step from the individual, to the species, to genus and so on.  Their coherence is directly associated with how close the correlation is and by this I mean that their lives are attuned to each other, that they tend to progress in a similar and supportive way, as if they were connected, because they are in a direct, intimate, though subtle way.  All matter and organisms are connected  via this encompassing field…coordinated and, in a sense, intelligent, purposeful…to everything else.  (An example of this can be readily seen in the ‘susurration’ of a flock of Starlings.  Not all animal species behave this way, but this behavior can be ‘explained’ by the coherence and non-locality made possible by such a field.)

Every function is coordinated within the cell and organism so that it may accomplish its many interrelated and necessary metabolic functions, its growth and maturation as an organism and, in the case of mobile animals, its ‘actions’, its movements in ‘space’.  Plants and animals, though their complexity varies widely from species to species, share this.  Internal functions are not random or chaotic, they work in proper sequence, choreographed, effectively and efficiently…with a degree of simultaneity when necessary, and purpose, to be alive.  Without this ability an organism would not ‘exist’.  It would be neither able to grow nor sustain itself.  It might fail to function at all or, at the other extreme, explode in an uncontrolled cancerous burst of growth.  In general, organisms don’t do this, at least they don’t until they pass maturity and begin to senesce, their various structures degrading, or under attack, become too stressed to continue or possess some genetic defect.  As long as it is able to continue living within its defined and specific parameters, in other  words, as long as it is able to maintain its own integrity as an organism, it will exist and ‘participates’ within this living ‘field’.  It is more than mechanical, it is more than, if you push on one point, you push on all points, it  is quantum and instantaneous.  The energy that constitutes this field would seem to be unavailable in the classical sense, one in which when utilized transforms energy, producing ‘work’ while dissipating into lost heat, entropy.  How can discrete, individual organisms do this?  Quantum coherence is in effect at the cellular and organism level and some argue at a universal level.  Coherence and correlation extends to other species, influencing, in-forming their relationships.  Physicists refer to  ‘non-locality’, as coherence that occurs despite physical separation, and it can do this because of this ‘field’ within which everything else exists.

In the quantum world of living organisms the old classical rules of mechanics are inadequate.  Organisms are not ‘machines’ responding to forces in their move to ‘equilibrium’, stasis and death.  Living organisms are in a continuing state of ‘disequilibrium’, energized within a ‘field’, filled with potential, in which tiny changes/forces/catalysts result in a ‘change’ in ‘state’ or position with relatively little expenditure of energy.  The metabolism, respiration, all of the internal functions of the cell and organism, ‘work’ to maintain the integrity of the living organism, allowing it to remain actively participating within the field.The organism and the field ‘work’ together.  This is an organisms tendency toward a state of ‘health’ vs. dissolution, entropy and death.

This is the living world envisaged by quantum physicists, a world that satisfies more of life’s questions than the old world of Newton’s classical physics which is better suited to simpler systems that operate in the world seeking ‘equilibrium’…a world that is more dissipative though fully capable of existing side by side with the quantum world.  One is static the other is alive.  Despite what fantastical machinations steam punkers might suggest, living organisms cannot be duplicated from wood, metal, glass and leather.  Such a built ‘organism’ would over heat, burn up, if it were required to metabolize every calorie of energy required for even its simplest functions.  Scientists have made these calculations.  The answer lies in a world of quantum organisms existing within an energy field in a constant state of disequilibrium.  Organisms in a state of equilibrium are by definition, dead.

After a long discussion with friends about this and related topics, one asked me just what is this ‘field’?  He wasn’t going to let me get by with just stating it as an ‘answer’ to the question behind life.  Okay.  Science ‘advances’ by attempting to answer such questions.  It purposes a hypothesis, an explanation, that it can test, in the form of an experiment.  Experiment’s are generally provable when we can ‘control’ for other variables so that a result will demonstrate that what actually happens, the change that we measured, can be attributed to the variable we tested for and not something else.  This is very difficult to do in complex systems, even more so in living organisms, because there are so many variables in play that cannot be controlled during an experiment.  This difficulty does not stop us from proposing hypotheses.  In such cases scientists have developed ‘thought’ experiments which are tested by their ability to withstand the scrutiny of examination by formal logic and mathematics.  Such theoretical experimentation often precedes our ability to perform a more classical experiment which has to wait until later, after materials, technology or a more formal groundwork of understanding is developed.  Absent this we have traditionally fallen back upon ‘belief’, a widely accepted worldview, story or explanation, in this case a new cosmology.

Typically, in a thought experiment, a hypothesis is proposed and tested by its ability to ‘explain’ the ‘problem’ or ‘problems’ that established theory has been unable to.   A classic lab experiment with controlled variables and measurable outcomes can be performed only when there is a degree of understanding of the context enabling scientist to fit it into a larger whole…but when the ‘whole’ itself is poorly understood, when our technology is inadequate, this may not be possible.  Science has made much of its progress by using reductionist thought, breaking problems down into smaller, controllable, problems.  This can only get you so far when trying to explain complex systems and organisms.  Such is the case when science looks at questions surrounding life?  There is too little clear agreement around this question.

 

In quantum physics they speak of quantum ‘entanglement’, which most simply refers to how quanta, the elemental particles of atoms, the vibrating ‘strings’, are intimately connected or entangled with each other…non-locally.  In other words, quanta are directly connected to each other within cells, tissues and organisms…to all things with which they are correlated, that they respond as one simultaneously, instantly, they vibrate or resonate harmonically.  The entire universe behaves in a responsive, complementary way.  As recently as one hundred years ago scientists used to speak of the vacuum of space as if it were empty, but now we know that isn’t true, for the universe is itself a vast ‘sea’, a media, within which everything exists.  Ervin Laszlo calls this the Akashic or A- Field, after mystical traditions of old.  Physicists speculate that it is super-dense, super-fluid and frictionless, composed of both energy and ‘information’; ‘superfluid’ and dense because objects within it create ‘waves’, patterns, that are transmitted throughout, directly and instantly, effecting all things within it; frictionless, because these patterns don’t ever dissipate, they continue, ‘interfering’, or interacting with every other creating complex patterns, of ‘memory’…literally…a memory which in turn subtly influences, informs, what is here now and what is to come.  Resonant.  The energy within this field is shared with matter and organisms, helping them sustain their conditions.  In organisms it helps maintain their state of dynamic disequilibrium, much as it does the orbit of the Earth about the Sun which would have degraded long ago crashing it into the Sun.  The field itself is dynamic, an active ‘participant’ in the ongoing universe.

Many scientists refer to this as the ‘zero point field’, ZPF.  It is immeasurable, beyond our direct perception, available to us only indirectly through the ‘behavior’ of objects and organisms.  The world that we directly perceive, effectively ‘swims’ within this as a fish does in water. It is all inclusive, expansive, including the entire universe, a ‘living’ and evolving bank of ‘memory’, information, and energy, energy estimated to be several times greater than that attributable to all of the visible matter in the universe, and information, connected back into all matter and organisms.  This idea fits well within the understanding of quantum physics which understands matter itself and by extension organisms, as structured, informed, energy itself.  When you break matter down into its smallest bits, you are left with energy.  Organisms are closely correlated energized structures, that resonate within the A-field.  The A field directly effects that which it contains and, in turn, is effected by that which it contains.  Some attribute to it the ability to form matter itself when it is suitably ‘informed’, energetically, by the other fields, gravitational, electromagnetic  and various quantum and nuclear fields maybe even by consciousness.  It is a complex ‘music of the spheres’ if you will, with a great many parts being played, harmonizing and ‘animating’, though each part is unique and each player, in turn, is capable of influencing the whole in a system of universe wide feedback loops, the whole, moving through time and space, directional.  Geneticist, Mae Wan-Ho, describes it as a kind of free form fusion of jazz with players ‘improving’ within the structure of the music.  They are coherent, in tune with one another, resonant.  Matter and organisms existing, living within this, individual players, participating and ‘in-formed’ by a universal, infinitely correlated system, that connects all matter, energy, even consciousness.

As ‘fantastic’ as this may sound such an idea explains a great many inconsistencies that keep surfacing under the old theories.  Classical mechanics, the Big Bang and relativity, miss a huge portion of the basic underpinnings, the foundation, of the universe.  Whether scientists are studying the ‘birth’ of this universe or the inner workings of the cell, the current paradigm, repeatedly comes up short.

 

Waking Up to a New World

Quantum theory, our difficulty in understanding it, puts this conflict between sense and understanding front and center.  We ‘know’ what we see…but do we?  Vocabulary, habits of thought, our ‘experience’ and education levels, all influence how we perceive and see the world…these things go to determining what we are ready and prepared to see.  When we look out we confirm much of what we already believe about it, or learn to ignore what doesn’t fit, and rule it out as anomalous and so, devalue it.  We all do this to some degree and find ourselves uncomfortable when others around us push unwanted ideas upon us that would require us to change.  Scientist can do this as well, but the method, by which they work, by which theories are tested, reviewed, accepted or rejected, demands an openness that we as individuals are less comfortable with.  We all have a desire for the solidity of a fixed known world.  To believe otherwise is to accept a little more chaos into our own lives.  We need to understand that what we ‘see’, in a very real sense, is a choice.  I encourage those of you who have made it this far to ‘read’ the book Unflattening by Nick Sousanis.  It takes a look, through both written text and illustration, at the world around us, asking that we open ourselves to new ‘dimensions’ of thought and perception.  We cannot learn if we rigidly stick with that which we already ‘know’ and believe.

Plant cells, all cells, go about their business, metabolizing, respirating, dividing, coordinating these functions, in very similar ways.  The cell is the basic building block of life, some are capable of independent living as individuals while others have organized themselves into massive multicellular organisms with highly specialized tissues and structures within them.  Each is ‘coherent’ and coordinated within itself and that is perhaps the most distinguishing characteristic between them, their ability to function as quantum, coherent, organic and animated structures…their lives a result of this.  I do not need to know where in an organism’s chromosome the precise bit of ‘code’ for a particular trait can be found.  I don’t need to know how each particular cell ‘knows’ which part it needs to successfully duplicate, to grow or replace, in order to reach maturity and maintain itself in a healthy state.  Or, ‘how’ exactly all of these individual genes ‘tell’ a plant’s ‘story’, a story that each individual interprets and expresses for itself in the process scientists study called ‘epigenetics’.  Certain genes are replicated, others are silenced resulting in unique tissues and organs, individuals, while the genotype stays the same…these are natural processes that do this, but can be effected by the environment and the organism’s state of health/disease…and by the ‘A-field’.  An organism’s genotype is a story, or script, that is interpreted uniquely for each individual, like a musician does a piece of music, the same notes, the same rests, or deftly altered, recognizable as the same ‘song’, but different, an individual expression.

Life is self-organizing.  The individual, while perhaps beautiful in its own way, is not of ultimate value, though each is essential to the process of life, each will pass.  In other words, with life, it is the journey that matters, not the destination.  The destination is momentary.  Relationships are built upon.  So, in a sense, it is the continuously unfolding story that matters…and that it continues.  Over emphasis on one moment, on one individual, is an error and devalues all of the others.  There have been many billions of individuals, billions of generations in the evolution of the cell, and there will be many, many more.  If this work of science can teach us more of our own humble and miraculous roots, then it will have succeeded.  We can measure this success by how we choose to live our lives, by how we garden, because understanding comes only after we have translated this into our own being, into action.  The miracle of life is all around and within us.  What more lofty goal could science have?

Looking Ahead

If we are to understand the ‘New Phylogeny’ of plants we need to understand what a plant really is, not just our own personal relationship with them in our gardens or the landscape beyond our yards.  For many of us the world of taxonomy is an esoteric one, that we take on faith or simply ignore…we can, after all, tend to our gardens and plants without cluttering our minds with the abstractions of science and its seemingly philosophical hair-splitting attempts at organizing the entirety of living organisms.  This is selling it and ourselves short.  The ‘intention’ of the Angiosperm Phylogeny Group’, APG, the scientists behind this, is both more grand and essential.  To understand what they are doing requires that we, as gardeners, as people, have a better understanding of their work and of just what these plants we are choosing to grow are and how they came to be.  It demands that we look a little deeper and come to know them as more than ‘green’ decorations for our yards and landscapes.  When we garden we do not merely ‘dabble’ in a large scale paint by numbers kit, we do so in a way that effects the larger world and the conditions by which our plants live or die….And, like so many other things, we do so as ‘insignificant’ individuals, with an accumulative impact, combined with our way of living on the planet, that is proving to potentially be one of the most destructive, in terms of life, periods in the entire history of Earth.  My intention here is to help ‘wake us up’ to the incredible beauty of life, a life that most gardeners are already aware of, but going further to the level of the cell, this miraculous building block at the center of all life, that has been evolving, perfecting itself, over the last 4.6 billion years.  Life is no random happening and its existence should not be taken as a given, capable of withstanding anything and everything that we might do to it.

[The next installment in this series looks at the evolution of plants, getting into the ‘meat’ of what the APG is considering in their reorganization efforts and nomenclature across all species.]

[I am adding a short qualifier here, for those of you with more academic expectations.  This is my own ‘synthesis’.  I read from diverse sources and have always been driven to understand why things are as they appear to be.  Experts, by definition, must choose what they focus on.  I don’t have to.   I am fascinated by the work of science and, due to science’s often narrow and necessary focus, can become frustrated by it as well.  I am an intuiter, a combiner of ideas.  I can be guilty of putting together ideas that experts often would not dare to do.  I am not worried about being 100% correct, of being able to document every connection or claim.  I look at things as fascinating puzzles and am driven to make sense out of them.]

A Select Annotated Bibliography

My thinking on life and evolution has been strongly influenced by my early readings, back into the 1970’s, of Pierre Teilhard de Chardin and a younger, at the time, generation of philosophers like William Irwin Thompson, David Spangler and Matthew Fox.  Their ideas of the noosphere, the ‘directionality’ and creative aspects of evolution, have had a long lasting influence.  All of these authors, and more, placed an emphasis on the creative, positive, forces involved in the creation and evolution of life, steering our primary focus away from the reductionist and negative ideas that dominate our culture today.  There writings can be loosely collected into a theme under ‘creation spirituality’.  They speak to the coherence and quantum nature of life and the universe.  Many others preceded them including the christian mystics..

Important, to me, in more recent years has been the writings of those like Dr. Lynn Margulis and James Lovelock, responsible for the Gaia Thesis.  Margulis, as a micro-biologist, wrote many books and papers on the development of life and the cell over her career which are quite accessible.  Microcosmos: Four Billion Years of Microbial Evolution, Lynn Margulis & Dorian Sagan (Margulis and Carl Sagan are his parents), University of California Press, 1997, is a good place to start.  Gaia speaks to the ‘directionality’, the increasing complexity and coherent nature of life as a ‘system’, the living Earth, and how its function is analogous to a single organism.  There is a consistency in operation across all life as different as individual species may seem to be.

Cells, Gels and the Engines of Life, 1st. ed., Gerald Pollack, Ebner and Sons, 2001.  As daunting as this may sound, this is a wonderful introduction into the inner workings of the cell written by a University of Washington professor of bio-engineering with a gift for putting the technical into very accessible layman’s terms.  It is still not a quick read, not because of its jargon..but because there is simply so much that is new for us to grasp.  Here is a link to his lab’s website that continues to research the properties of water.  He has another accessible book still on my to read list, The Fourth Phase of Water: Beyond Solid, Liquid and Vapor.

The Rainbow and the Worm, 3rd. ed., Mae Wan-Ho, World Scientific Pub., 2008.  In this volume Wan-Ho discusses the quantum nature of the cell and the organic architecture of living organisms, the bio-chemical and electrical functioning of an organism.  Over the last 15+ years I’ve read each successive edition and glean something new from it each time.  Don’t pressure yourself to get it all on the first go….give it some time.  Well worth it!  There is a later title, Living Rainbow H2O, by Wan-Ho from the same publisher in 2012, that looks even more deeply into the essential role of water…recommended!

Science and the Akashic Field: An Integral Theory of Everything, Ervin Laszlo, Inner Traditions, 2004.  Laszlo is a big thinker, a now retired philosopher and systems theory professor, capable of discussing themes and theories from disparate fields in an understandable way.  This is a big idea book and sometimes he may delve a little deeper than you want into the details of physics, like the double slit experiment, but you can skim those and pick up the essential ideas.   The sciences today are beginning to widen their traditionally narrow focus and are creating theoretical bridges that are a great more explanative and comprehensible than early theories that are becoming more problematic.   He lays out the idea of the Zero Point Field, as media or background to the universe, a super dense, super energized media, ‘fluid’ and frictionless, conductive, coherent that is directly ‘entangled’ with matter, including organic life.  We cannot see it or sense it and know that it is there only by how it effects everything else.

Unflattening, Robert Sousanis, Harvard University Press, 2015.  Sousanis is Assistant Professor of Humanities and Liberal Studies at San Francisco State University.  He majored in mathematics and went on to become the firsts doctoral candidate at Columbia University to write his entire doctoral dissertation in graphic novel form.  His dissertation was later published as this book.  There is a whole movement, if you will, of scientists and artists, beginning to reach out to the public through comics, a graphic form, to present what has previously been inaccessible to the interested lay person.  Here is one such title, “Eating Anthropocene”, in which participating comics creators translated specific ideas around biology, geology, agriculture and food security, moving into a future of climate change and population growth.  It was developed at a symposium in Europe where comics are more widely accepted across age groups.   The link that follows presents all of the formal papers presented there and the idea.  “Science Meets Comics. Proceedings of the Symposium on Communicating and Designing the Future of Food in the Anthropocene”.science-meets-comics-ebook

 

 

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