What is Life, Biology and the Non-equilibrium State: The Quantum World of the Organism

Sometimes art does a better job of conveying ‘reality’ than does our direct experience as it forces us to look through the eyes of others. The swirling, blurred edges of Van Gogh’s work begins to show us something of the immateriality of the world out there as images bleed over their edges into others with a visual energy that a photograph cannot provide.

[Dear reader, if this seems a bit rambling, I’m sorry, but my first purpose here is understanding the role of Quantum Physics in the life of the organism.  This is me trying to make sense of it and I do this by writing.  In writing our errors become most obvious.  I have read and reread this many times, rewriting and editing sections, throwing others out I later decided were just wrong.  I suspect I will come back to this over time as I continue on this quest to understand this post’s central question and that should be okay, because my understanding, like the science I am reading continues to evolve.  I read fairly widely across the several branches of science and rarely find those who can integrate these ideas.  Quantum Biology is a real thing, but the work of synthesis or joining the pertinent work and theories from the separate sciences has really just begun.  Quantum mechanics, biochemistry, cell biology, enzyme action, evolution, metabolic activity, the unique role of the water molecule in life and the study of life as an integrated, complex system, is not something done.  It is my belief that to understand the miracle of life, one must have a grasp of the related sciences and their various complimentary and competing theories.  The story they each tell individually is, unsurprisingly, incomplete.  We will never understand life if we continue to examine it only in its isolated parts and functions.  Life is quite the opposite.  If you reader are able to gain some clarity from my struggles here…then all the better!]

What, some of you are likely thinking, does quantum physics have to do with biology and living organisms?  Physics’ realm, after all, is that of apples falling, billiard balls ricocheting off of one another, a planet orbiting around its sun, the electricity that powers many of our devices and nuclear explosions.  Yes, it is that, and so much more.  It examines and seeks to explain the physical properties of matter and energy in all of its forms and at all of its scales…well, at their most basic, tiniest scale, organisms are composed of this same matter, the stuff of planets and stars.  Quantum physics looks at this ‘behavior’ at unimaginably tiny scales, that of quanta, those tiny bits that physicists, like Max Planck discovered cannot be further divided, that contain fixed and set amounts of energy, that when multiplied by billions, gain enough size that we can directly perceive them.  At the tiny scale of quanta, of sub-atomic particles, the laws of matter change, those used to calculate the trajectory of a much more massive rocket or explain the movement of heat in water, no longer hold.  Such tiny bits of matter behave differently and such tiny bits play key roles within living organisms. 

At that level, all of these particles exhibit what physicists describe as quantum motion and uncertainty; they are capable of ‘tunneling’ and ‘walking’; of being in two, binary, states, particle and wave, at the same time; of having the potential for what physicists call ‘super-position’ or having the capacity to possess different properties at the same moment until they are caused to ‘collapse’ into a single state, a single position; and they do this at a scale well beyond our ability to directly perceive, that of nanometers and time frames of nanoseconds, billionths of a meter, billionths of a second.  These are the scales at which we could examine single atoms.  At such scales quanta, the component bits of atoms, the smallest atoms, like hydrogen, common to virtually every ‘organic’ molecule, ‘behave’, can do these things, coherently, as if they were directly linked and coordinated.  This is a ‘world’ in which velocity and location become problematic, in which a particle/wave cannot have its velocity and location known at the same moment, a world in which quanta could be in more than one place, at the same time, no, ‘are’ in any of several possible positions at a given moment, a world of ‘probabilities’, where in a very real sense all things are possible.  Physicist’s speak of ‘wave forms’ which are predictive tools to help them determine the probability of one’s velocity and location….What?  Such ideas boggle the mind.  At such an unimaginable level, matter does not exist, not in the kind of solid, fixed, massive sense that most of us tend to think anyway.  At that level matter consists of energy, that is ‘informed’, structured in such a way that through its energized action, its ‘behavior’, ‘wave forms’ collapsing in and out of ‘fixed’ position, manifest at our scale as the ‘stuff’ we know and can perceive.  This is pretty bizarre and ‘weird’ stuff.  Some refer to this as the quantum weird.

….This might be a good place to take a break…then reread the above.  The reader might do well to take this approach as your ‘work’ your way through this, bit or bite by bite.

Theoretical physicists, those that specialize in the strange world of Quantum Physics and the mathematicians with whom they often work, are busy working to figure this out, creating new ‘maths’ to ‘explain’ the behavior of matter in the universe, while their experimental counterparts develop new techniques and tools that work to give more direct evidence.  Together they are giving us predictive models for the ‘impossible’ things, that do happen at certain tiny scales.  More recently they have been working with biologists, while biologists have been considering the theories and ideas of quantum mechanics, looking within living organisms, to determine what role quanta may play in life.  Biochemists, who examine the nature and processes of chemical reactions within living organisms and the molecules which are a product of life, are doing the same, searching for better understanding of how these biochemical reactions within organisms can happen with such incredible consistency and efficiency. 

Quantum biology, an infant science, is still developing, rapidly, redefining many previously inexplicable processes, ‘magical’ actions, that take place within organisms.  By inexplicable, I mean processes that classical physics and chemistry have only been able to do ‘incompletely’ or ‘bluntly’, my terms. These include certain elements of photosynthesis, energy exchange and conversion, enzymatic action, the astonishingly accurate replication of DNA, RNA and proteins, the mechanisms by which organisms perceive scent and vision, the internal compass of some migratory species, even the function of our brains, memory and the concept of consciousness.  Classical physics and chemistry have been less successful in their descriptions of these processes when looked at closely.  Science is just now beginning to understand the role quantum physics plays in making organisms as they are today, possible.  There are key actions in all of these processes that come into clearer focus only when we look at the  ‘behavior’ of subatomic particles and the larger ions and smallest atoms which come together to form the larger molecules and structures that we can observe.  At the level of their component ‘parts’, organisms can retain these other capacities which, arguably, endow them with the possibility for life.

Most of us ‘live’ in a universe limited to the three perceivable spatial dimensions and the slipperier one of time.  We are limited in our thinking to those four.  We utilize our perceptions available to us, dependent as they are on our sensory organs themselves which are composed of atoms and thus unable to directly perceive them.  With them we render the world understandable, we come to “know” it, within these limits.  What doesn’t ‘fit’ inside of that becomes simply, inexplicable.  Beyond us.  Magical even.  We cannot see atoms yet we know they are there.  We possess the understanding and technology to ‘see’ them and measure their ‘impact’.  We have developed working theories that give us very accurate predictive abilities from studying them, but you and I, who are individually made up of literally many trillions of atoms, don’t possess the capacity to see or sense them directly.  For most of us these are truly baffling concepts, ones that are unsupported by our own experience.  For us sub-atomic particles and strings exist forever beyond our vision, our perception, barely even possible for us to imagine.  It is this universe of such unknowable dimensions where most of us get lost, and it is here where these ‘strings’ and particles ‘spin’ and move in ways that offer the ‘best’ ‘explanation of much of the universe, that give many of the properties and characteristics to the elements and compounds that compose the ‘knowable’, visible, world.  It is in the impossibly tiny and fantastically ‘curved’ spaces, at least for ‘superstring’ theorists, a topic I won’t get into here, which I understand even less, that matter comes into being, when ‘wave forms’ and possibilities converge or ‘collapse’ in just the right way that matter comes into being.  On this ‘foundation’ the universe is built.  ‘Choices’ are made.  Classical laws become definable. Probabilities ‘collapse’ into wholes, while in the next moment, literally measured in nanoseconds, these same particles participate in this quantum and dynamic state of movement and exchange, move and change within prescribed limits. 

Those diagrams and models you may remember from science classes, of little ‘balls’ held tightly to form the nuclei of atoms with other smaller balls, electrons, spinning madly in their own tiny orbits around them, larger atoms holding their electrons in several, each slightly more distant ‘shells’, all some how held together by electrical charges, but not collapsing into one solid object…are not the reality at all.  They were simple teaching models, developed before our understanding of quantum mechanics was very well understood.  These served their purpose explaining an incredibly complex topic as best we could.  Science, physics, is still working to more fully understand this.  To be sufficiently explanatory, that is, to explain what we now know to be true about matter and its capacities.  The ‘classical’ model of balls and discrete orbits is simply not true. 

The truth ‘is’ fuzzier.  Those ‘orbiting’ electrons with their negative charge, exist as a kind of cloud, a ‘smear’ existing in all of its ‘possible’ positions at the same time, not as a single electron in a discrete orbit,.  In order for the mathematics that underpin the physics to more accurately ‘explain’ the world, this subatomic world of probabilities, not fixity, must be.  That mug you lift to your mouth, the coffee itself within it, even your own body through which you are experiencing this, at its most microscopic level, exists in reality as a consequence, its ‘wave form’ collapsed, becoming this particular ‘now’, reality, in a very real sense.  Broken down into its constituent subatomic particles it would all ‘dissolve’ into possibility and probability again.  Under special conditions this coherent, quantum state, can exist within living organisms for moments, flashing in and out of fixity and solidity.  The position and velocity of quanta can only be determined by, what physicists call the act of observation, that observation causes sudden limitation, but not just the act of human observation.  Rather, my understanding of the concept can be more clearly understood as one of ‘relationship’, that once a relationship is entered into, a certain fixity is gained.  This ‘relationship’ is connected to the concepts of informed energy, and the architecture of matter, gaining more fixity as matter becomes more complexly structured, when it is acted upon by other bodies and forces.  Living organisms are incredibly complex structures with equally complex energy flows that work internally to allow a very controlled quantum dance of energies. 

Ultimately, what we believe to be ‘solid’ is not, the very energy that shapes and drives this, is not what it might seem.  Sub-atomic particles are structured into the form of atoms, atoms are organized into molecules of an astonishing variety and size and these then form into the many substances and organisms that comprise our, the visual, perceivable, world within which we interact, which compose our own bodies within which we exist…while at the level of quanta, they exist as unimaginable probabilities.  The world, the universe, life, in a sense, has ‘collapsed’, been reduced into particular possibilities and become what we generally perceive it to be.  With our limited perceptions we cannot truly ‘see’ what is out there. 

At each increasingly organized level of structure this energy, the quanta, are directed and contained, ‘observed’ and at that moment collapsed into a definable thing, giving each atom, molecule, substance and organism more focused, limited, predictable properties and characteristics.  The energy they contain variously transformed, amplified, blended or muted into more stable, repeatable patterns, patterns that have been ‘proven’ and become part of the repertoire, manifested, preparing the way for the next ‘step’.  These ‘chosen’ forms do not involve ‘decisions’ for us to make.  Mostly this structuring of matter tends toward stability, focusing the energies contained within its lower levels into nuclear and chemical bonds working within the realm of classical physics and Einstein’s ‘relative’ universe.  It does not supersede other forces.  Gravity, classical mechanics, thermo-dynamics and electro-magnetism…it works ‘beneath’, in the background. 

Molecules and substances tend to be conservative and require added energy to break them.  Non-living matter, that of minerals, gaseous and fluids, are often simpler in their structure such as in mineral crystals. They possess a density, stability and physicality, that we might identify as more limited and fixed, changeable with the addition of outside energy, non-living…but they still contain and in fact can be defined by the energy within them.

Many ‘solids’ when heated change phase to a liquid state, their instability, exhibited in their ‘fluid’ motion, though still not alive.  Add enough more heat and these will again switch phase into a gaseous state.  Each substance does this at its own prescribed temperature.  The have melting and boiling points.  Most change from one phase to another at temperatures well outside those within which we could exist as living organisms.  These states all exist under particular ambient, given, conditions, pressures and temperatures.  Change these conditions and you begin to change all of the countless patterns that support the more complex levels above them.  Stable states are all about containing, limiting, these internal energies, their ‘freedom of movement’…but such energies never go away….Einstein’s famous equation, E = mc2, gave us the understanding to create the atom bomb, the idea that matter itself contained unimaginable energy.  Much slower to follow has been our understanding of what this means for matter in general and the nature of the world around us, of matter at its quantum level and the animating force that it can be when structured, configured, in just the right way.

When the layperson, regardless of their education level, comes upon these ideas, we face an incredible stumbling block, the highly specialized language used to describe the science behind this.  It is foreign to our experience.  For a scientist schooled in the jargon and its precision, they face a mirrored nearly impossible task to explain what they know to the layperson.  Without the precision of language the concepts remain more fuzzy and as our familiar, accepted, daily reality seems to contradict their ‘fuzzy’ ideas…which aren’t ‘fuzzy’ at all, we easily reject or ignore them.  Their thinking and language is extremely focused and precise and demands a level of critical thinking and a willingness to suspend our commitment to our own vision, familiar as it is, to examine it more closely.  There is a saying, “To a hammer, the whole world looks like a nail.”  This speaks to our tendency, our reluctance, to question what we have been ‘taught’, what we have ‘learned’ to expect, our ease to accept our biologically limited perceptions of the world that we live in, even when that understanding of the world is demonstrably ‘wrong’ or incomplete.  We ‘learn’ to see the world as we do. 

Our brains have evolved in such a way that we blur and blend visual stimuli in a particular and shared way so that we can detect physical threats, respond and warn others to avoid danger and provide a shared, mutual defense, as well as to determine what is positive or safe.  They provide us with information to act on and to make decisions on.  These abilities are critical to survival.  Vision and our other senses allow us to make sense of the world putting it into ‘context’.  We create an ongoing ‘story’ linking what we sense right now with what we ‘remember’ from before to ‘make’ sense of it.  We see discrete forms and remember them, interpreting them as we go, imagining it to be ‘real’, that it is what is there and what others see….Each of us live in a world ‘dressed’ in story and to the degree that we share the same story we share the same vision and understanding.  When we don’t, miscommunication happens.  When the story is ‘wrong’ or incompatible with that being told to us, it becomes an impediment.  Some of us are intrigued by this, but most of us reject such conflicts and attempt to avoid being overwhelmed by their implications.  That which once served us now limits us.  This is where much of us are hung up today and where we need to move beyond…no small or easy task.

Each particle, each element or molecule has a different energy ‘signature’, a different mass with its associated properties of charge, volatility, attractions and repulsions, melting and boiling points, with tendencies for very particular associations based on these and their physical structure.  Compounds are formed, later to be transformed by changed conditions, such as the accumulation of shells into limestone and later, under great heat and pressure, into marble, stone bearing very little resemblance to the creatures who once wore the shells of which marble is ‘made’.  New possibilities can result in new paths, yielding new outcomes which in turn open the door for even more possibilities, each built on the success of previous paths followed. 

Living as a Balancing Act

Living organisms opened up a world of entirely different possibilities, beginning from a long chain of protean innovations that science is still attempting to figure out.  The process could be described as one of innovation, testing and ‘learning’, followed by another innovation in an unending cycle.  Each ‘stage’ of this process must have been successful in order to lead to the next.  Failure would mean death and the end of a line.  The answer to the Chicken and Egg question has to be…both, every time.  Although that chicken and its egg were evolving in their complexity, each generation must have been successful enough to produce the following.  Again, with out the full story available to us we have trouble imagining how this could be, stuck as we are on the chicken before us and those fossilized progenitors we have available in the geological record.  Somehow they string together.  There is also the issue of ‘new’ species appearing over vast stretches of time, linked genetically to earlier species, the intervening ‘story’ missing linking chapters.  There is no such thing as spontaneous generation.  Life has never appeared from nothing.  Something always precedes it.

Science struggles with this as do we individually.  The process though, of evolution, of innovation, is a combination of previous successes, of DNA shared and reconfigured or as bits of an organism’s genome, recognizable in some cases today as plastids, in different organisms through the process of horizontal gene transfer, then tested by the conditions and requirements of life which are very tightly delineated, living on one side, dead on the other.  Each ‘innovation’, each new individual, must resonate, energetically in such a way as to remain viable, its structure, fully integrated and coherent.  Abnormalities too far afield result in an energetic collapse of the structure and the individual’s death.  Each organism, as you go up the ladder of complexity, requires coherence in its parts and as a whole.  Arguably, it began and continues to rely on particular physical/structural relationships. 

The Cell and Its Composition

Ours is described as Carbon based life, all of an organism’s cells and macro-molecules contain some amount of Carbon.  Carbon is an essential component of these macromolecules.  These include proteins, lipids, enzymes, nucleic acids, and carbohydrates. Carbon’s molecular structure allows it to bond in many different ways and with many different elements.  There is no life form, we are yet aware of, that is silicon based or based on any other element. 

These ‘organic’ molecules come together to form the common cell.  Within the broad sweep of living organisms the singular structure of the cell is shared.  Whether Fungi, Plant, Animal or Protista, the basic structure of the cell is shared.  While cells vary, the cells of any organism share an essential structure and operation, whether that of an Amoeba, a Sword Fern or a Human.  Each is bound by a cell membrane, contain cytoplasm as well as a cytoskeleton and DNA.  Bacteria and other Prokaryotes, ‘Pro’ being the latin for early as in the word protean, are simpler and of more ancient origin.  Eukaryotes, ‘Eu’ being the latin for true, evolved much later, have longer, more complex DNA which is contained within a nucleus with its own protective membrane within the cell.  Eukaryotes also have varying numbers of smaller organelles within their cytoplasm which perform specific functions.  All living cells function in shared ways utilizing very similar if not exact basic processes.  Each individual cell of each species is defined more by its similarities than differences.  This is true for any organism you choose to examine. 

Each cell depends on relatively few elements that compose the bulk of the ‘biomolecules’ that collectively make them up, six: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous and Sulfur, often referred to in biochemistry as CHNOPS, being the most common.  Not every biomolecule contains all of these and the 20 or so other elements found In less numbers.  Proteins and the 21 amino acids that comprise them are composed primarily of the first four with three containing smaller amounts of Sulfur and Selenium.  In the plant world we utilize fertilizers which contain Nitrogen, Phosphorous and Potassium, sometimes with trace elements, various metals needed only in very tiny quantities, too many of which would be toxic to living organisms.  Fertilizers needn’t contain Carbon, Oxygen or Hydrogen, they are abundant and readily accessible from the atmosphere and water. 

[Nitrogen, an atmospheric gas, is also ‘available’, but most organisms require ‘help’ in getting the highly water soluble form of it that they can utilize.  Under typical conditions in our gardens and agricultural fields Nitrogen, because it is very water soluble, washes down beyond the reach of the roots of crops and so must be ‘recycled’, held in one organism’s tissues taken up by another as either its food or from its decomposing tissues, unless a plant has an association with a particular nitrogen ‘fixing’ organism which can capture it directly from the air available to it diffused through the soil.  Soils which are home to well balanced and complex living communities hold the nitrogen in their living and decaying tissues.  Monocultures, because they lack this integrated living community generally require the regular addition of nitrogen rich fertilizers.] 

Other elements are necessary in certain specialized cells and metabolites, those compounds the cell creates itself, such as  ATP, Adenosine Triphosphate, the organic ‘battery’ used to power countless processes in all cells.  Others like Calcium, Sodium and Magnesium are utilized to maintain the pH, which refers to acidity or alkalinity, determined by the proportion of Hydrogen ions, H+, dissolved in the water within and between cells.  pH strongly effects an organism’s rates of respiration and metabolism, limiting and facilitating the capacity to carryout its  bio-chemical reactions.  Some trace elements partner with specific long chain protein molecules which function as reaction sites of various enzymes or catalysts, making otherwise impossible chemical reactions in the body, possible, allowing them to overcome the energy barriers within the cells in a coherent and coordinated manner.  Some scientists refer to enzymes as the regulators of life facilitating and limiting the melange of processes going on, often simultaneously, within all cells, tissues and organs.…And, of course, there is water, essential water, that singular and unique molecule which is central to all of it.

Water, the simple H2O molecule, is not so simple.  It serves central roles in both the creation of first life and as a solvent, as a facilitator and source of material for ongoing life and evolution and as an energy source.  Water is a unique molecule in the universe and every organism, every cell, carries with it its own bit of the primordial sea, protected within its epidermis and cell membranes..

Water molecules and their behavior are central to the complex path that life has followed….Water possesses a unique fourth state, that of denser, liquid ‘crystalline’ water, a more structured, phase of still ‘liquid’ water, that under certain condition can be induced, literally transforming the molecule itself and setting into motion actions necessary to life and the cell.  Interestingly, and uniquely, the ambient conditions on Earth, its range of temperatures, have stabilized at such a level as to ‘bracket’ the liquid state of water, in which its fourth phase is possible.  Were it significantly colder, or warmer, across the vast surface of the Earth, or if water itself were only liquid outside of this range…life would not have occurred here.  Water is strongly dipolar, it contains a positive and negative pole, a charge, that gives it unique capacities to bond with other molecules and atoms, giving it its capacity as a ‘solvent’ when in its liquid state, making it capable of dissolving and thus transporting other elements and compounds required by organisms.  It allows for the possibility of ions, charged atoms, that are essential within the chemical process of an organism. 

Transitioning into and out of the fourth phase involves the release or absorption of energy, in the form of positively charged hydrogen ions.   When water molecules are adjacent to proteins and light energy is available, the water molecules are energized and restructure themselves, giving up H+, ions, the remaining molecules, now with a negative charge, bonding  to each other and the protein in such a way that forces the former dissolved ions out of solution and into the flow of protons away from what Gerald Pollack has termed the ‘exclusion zone’ adjacent to the protein, the rearranged and modified water molecules now tightly packed and bonded to one another, excluding other ions.  This both sets the stage and helps power the cell and organism.  It creates within the organism a ‘charge differential’, creating a state of ‘disequilibrium’, of dynamism, in which ions, charged atoms and molecules, play an important role, working with enzymes as catalysts and switches within an organism.  (Please see my earlier post and look into Gerald Pollock’s books, “Cells, Gels and the Engines of Life” and “The Fourth Phase of Water: Beyond Solid, Liquid and Vapor.”  Those near Seattle’s UW try to attend some of his lectures on the topic or check out his videos.)

The structures of atoms, molecules, and in the case, of living organisms, of macromolecules like proteins, all contain energy/information, ‘added’ when they’re formed, subtracted/lost when their structure breaks down…always.  The ‘construction’ and ‘folding’ of proteins within the cell’s many ribosomes found throughout the cell and concentrated within the smooth and rough Endoplasmic Reticulum and Golgi Apparatus, is directed by RNA which serve as ‘templates’ and are modeled directly off of portions of the cell’s DNA, precisely.  They are not random, cobbled together, structures.  RNA are ‘information’ heavy ‘plans’ for the proteins.  Some of the specific operational information of this process is carried within the ribosome’s own DNA separate from that within the cell’s nucleus.  You need some understanding of the scale of this problem.  Organisms range widely in size from a single cell to humans composed of billions to those much larger than us.  Each cell can contain several thousand ribosomes producing and reconstituting specific proteins for that cell.  Each ribosome can produce thousands of proteins in a very short time from.  Each ribosome must contain viable RNA sent to it from the Cells nuclear DNA.  Each RNA molecule lasts only a few minutes, at most, before it must be replaced.  This is an incredibly complex process, that again, must operate within a very narrow set of parameters to continue living.

Each protein, each RNA molecule, requires a near impossible level of precision, while produce in such mass quantities that boggles the mind. Each of these includes the same degree of organization and focusing of energies.  This is anything but a simple assembly line process.  Such complexity and scale begs that we accept and understand quantum processes. 

Simple structures tend to be more stable than complex ones, whatever their ‘state’.  Matter that is organized into the biomolecules of living organisms, ‘lives’ in a state of ‘disequilibrium’, ‘balanced’ by a steady flow through of energy helping balance the organism.  A healthy organism possesses a level of ‘vitality’, or balance, a conservative stability and dynamism.  Living organisms utilize energy to power and maintain themselves, aided by their DNA, but also ‘directed’ by the precise structure and capacities of the organism itself in a direct feed back loop, the management of which some might describe more as a quantum computer type process.  ‘Dynamic stability’ is an active living state of the organism.  This complexity increases as you move from bacteria, to archaea, to single celled eukaryotes to more complex, multi-celled species, but it is there in each.  Each increase in complexity ‘complicates’ this process, making it more consumptive of energy, making such species seemingly more ‘fragile’ and prone to failure, yet this dynamic balance, this yin and yang, finds a pathway through it.   An inherent instability, balanced out with an information heavy conservatism, an instability that is continuously perched on the edge between life and death.

The Necessity of Energy for Life

Living organisms require a continuous flow of energy to maintain their living state, more if they are to grow and reproduce.  Organisms must all consume energy.  In the case of photosynthetic organisms they ‘harvest’ this from sunlight. (As always there are a few exceptions including parasitic and hemiparasitic species that rely on others for some or all of their carbohydrate requirements).  Some, much more rare organisms, accomplish this by consuming, oxidizing, other non-organic materials, not carbohydrates, breaking their chemical bonds and utilizing the energy released in their own internal processes. Animals, fungi, bacteria and non-photosynthetic plants must gain their energy from other sources by consuming them, primarily plants or, secondarily, by eating animals dependent upon plant consumption.  Organisms use this energy to power virtually all of their internal processes, metabolizing the compounds held within the cells and tissues of other organisms, ‘breaking’ those down to capture the energy within their bonds while utilizing at least some of the complex molecules gained in their own processes.  The rest is excreted as waste.  Organisms literally live within a complex field of energies, all of which are essential to their being.

Chemists and bio-chemists often argue that life is driven by the process of oxidation, the breaking down of compounds, turning more complex molecules into simpler ones, releasing the energy once held in their bonds.  Oxidation is what happens when wood burns.  Wood can sit for years without bursting into flame.  The Oxygen, the O2, is certainly adequate in the atmosphere, but there is an energy barrier that must be crossed before the wood ignites.  For paper that is 454ºF…that doesn’t happen without an outside input of energy.  Once ignited the fire continues until the fuel or O2 are exhausted…or the fire is cooled.  These energy barriers exist for many thousands of organic compounds and molecules.  Without such barriers organisms would experience spontaneous combustion and burn to ash.  Controlled oxidation energizes living organisms, so we have a bit of a conundrum which is overcome by enzymes. 

Enzymes and the Role of Heat in an Organism

Organisms do not operate like mechanical/heat engines.  While organisms ‘burn’ fuel, it is not the explosive process of combustion.  As I wrote above, their rate of oxidation is controlled by enzymes and occurs at much lower temperatures than does classic carbon combustion.  A heat engine, whether it operates consuming wood, coal, diesel, gasoline or any other combustible fuel, creates explosively expanding gases with large and rapid releases of energy, of heat.  Such engines utilize the large differences in heat produced within the engine and the outside air into which it is exhausted.  This heat differential drives the engine and produces mechanical work.  A very large portion of the heat is ‘wasted’ exhausted before it can do work. 

In an organism the heat produced from oxidation of their ‘fuel’ is secondary.  The relatively small amount of heat is lost to the environment while the ‘charge potential’, the now positive and negative charges created via this ‘breaking’ of chemical bonds, is conserved, capture in the organism’s processes.  The now divided molecule’s ‘parts’, charged and highly reactive, are directed through a cell’s internal processes, combining with other selected molecules, to form more useful and stable molecules, sometimes utilizing this charge differential in a chain of compatible and purposeful reactions.  In some reactions, such as the phase shift in water discussed above, H+ ions, protons,  produced by the breaking of its hydrogen bonds, leave them free to be utilized in other processes. 

In the numerous and essential mitochondria of cells the flow of positively charged protons, H+ ions, power the complex ATP synthase enzymes which physically drive the recharging of ADP, adding an inorganic phosphate to ‘reconstitute’ the ATP molecule which carries a negative electrical charge, useable by countless sites within the organism, the use of which then knocks a phosphate atom free, necessitating its recharging, back at a mitochondria. 

The rate of all chemical reactions are effected by the ambient temperature under which they occur whether in a lab or within an organism.  Plants and many animals, including insects, fish, amphibians and reptiles, are ‘cold blooded’ or poikilothermic, their metabolism rates are directly tied to, limited by, the surrounding medium’s temperature, air or water, which the organism’s internal temperature tends to mirror.  They do not have the capacity to warm and stabilize their internal temperature at an ideal rate.  They have evolved, more dependent upon the ambient temperature of their environment.  They also lack abilities to cool themselves should the ambient temperature rise too much.   Within these limits, their metabolism adjusts with the outside temperature.  In plants their metabolism can virtually slow to near zero when it drops too far or rises to high, effectively inducing a kind of dormancy in some cases or, if severe enough, cell and organism death. 

Fish, living as they do in water, with their high complexity and energy demands are more quickly effected due to water’s heat conducting property.  Fish, like the NW’s salmonids and trout, which require relatively cool water temperatures for spawning and survival, are seriously compromised  by even relatively minor rises in temperatures such as those caused by removing the forest canopies which shade and cool the streams they occupy. 

Whether poikilothermic or warm blooded, or homeothermic, an organism must maintain its tissues within limited parameters for metabolism to continue and support its cellular requirements.  Where ‘cold-blood’ organisms are entirely dependent upon ambient conditions, a good portion of the heat produced by the increased respiration of homeothermic organisms is utilized to help maintain optimum internal conditions for the organism.  Homeothermic animals, mammals and birds, also possess some capacity to cool themselves when temperatures rise too much.  Even for homeothermic organisms heat doesn’t ‘power’ them, it is the negative and positive charges captured from the oxidation and other biochemical processes that take place within the organism, the breaking down of more complex molecules, that result primarily from their respiration, the oxidative process of ‘burning’ their ‘fuel’ with the available O2.

Sugars’ Roles in Organisms: fuel, antifreeze, antidesiccant & structure

Photosynthesis captures the energy of individual photons, the incredibly tiny energy packets within light, that quantum physics has looked at so closely, and stores that energy within the sugars created within the plants.  Different species form several different sugars, in different proportions, which are transported around the organism to tissues and cells where they are needed.  These several sugars, sucrose, fructose, glucose, dextrose, lactose and others, perform varied services within the organism.  Glucose is the primary fuel for cellular metabolism.  As needed sucrose, which is a compound of fructose and glucose, can be broken down, if the organism possesses the enzymes to do this.  The same goes for lactose, no enzyme available, not oxidation of lactose. 

Plant sugars perform various other functions among them being as a kind of anti-freeze protecting living cells from catastrophic damage that could otherwise occur when their contained water freezes into crystalline form.  The sugar content in the plant cells and vascular tissues of many plant species from temperate and colder regions, tend to increase as temperatures drop, effectively lowering the temperature at which cellular water will freeze.  The production and concentration of the controlling enzymes change with them.  In other plants, sometimes the same, dissolved sugars increase to limit damage caused by drought and consequent desiccation of its tissues, in a few cases, like those plants commonly known as ‘resurrection’ plants, enabling them to recover from losing virtually all of their ‘available water’, though most plants would suffer catastrophic damage and die well before this. 

Essential to the existence of all organisms is another type of sugar.  All organism’s chromosomes contain deoxyribose, a 5 carbon sugar that formed into a long chain matched with phosphate molecules, forming the ‘rails’ that provide the framing structure of DNA’s double helix.  RNA, which are working copies of specific segments made off of DNA, are strung together along a single ‘rail’ of another form of ribose sugar.  These particular sugar structures form a stable scaffolding, especially that of DNA’s deoxyribose, which must maintain its structure precisely over generations withstanding the oxidative conditions within the cell.  RNA is shorter lived and must be produced in incredibly large quantities to guide the development and maintenance of every cell.  RNA carries the genetic information to a cell’s thousands of ribosomes where the organism’s proteins are created. Later many of these proteins are ‘fitted’ with particular metals and function as enzymes within a cell’s metabolic processes.  To get a sense of their role and ubiquitousness, consider that the bacteria E. coli, which is much smaller and less complex than the Eukaryotic cells that comprise animals, plants and fungi, can contain a thousand different enzymes at any one moment each with its specific long chain protein and reactive center.

The Role of Enzymes

Enzymes are literally the key to everything going on within a cell and organism.  It is only glucose that once carried to a cell is oxidized, ‘burned’ in the presence of O2 , to release their energy which is converted into ATP, which I won’t get into here.  Other sugars and compounds are utilized for other purposes and require their own enzyme to facilitate those reactions.  Still other enzymes enable a cell to build new compounds, overcoming other energy barriers that prevent them.  Enzymes are made by stringing together between 100 and 1,000 amino acids in a very specific and unique order, into proteins. These chains of amino acids are then ‘folded’ into a unique shape. That shape allows the enzyme to carry out specific chemical reactions, they ‘catalyze’ more than 5,000 different reactions…and it may require a sequence of specific enzymes to catalyze each step in more complex reactions.  The point I’m making here is that many of these biochemical processes within the organism are regulated by particular enzymes.  No enzyme, no oxidation no reaction.  Enzymes all serve as keys, as ‘matchmakers’ in a chemical process, ‘matchmakers’ that show up at just the right time, their precise physical structure ‘meshing,’ in this case with a specific sugar’s, recognizing it.  With the enzyme present the energy barrier is lowered and oxidation happens without need to raise the temperature above that of the barrier.  Sugar does not ‘burn’ simply by being in the presence of Oxygen. 

This enzyme catalyzed reactions occur in both single and multi-celled organisms, all of them contained and coordinated within single celled organisms while these reactions and their enzymes may be limited to specific cells, tissues or organs in multi-celled organisms.  This is part of the complexity and specialization that takes place in more complex organisms.  In a way, single celled organisms seem more marvelous in their capacity to perform all of their functions, contained.

Enzymes are not directly effected by the reactions they catalyze.  They remain largely unchanged and available.  They work in conjunction with various inhibitors that block the reaction until needed by ‘binding’ the enzyme’s reaction site.

Quantum biologists and many  biochemists argue that quantum ‘fuzziness’ comes into play in these reactions.  Biomolecules are held together by shared or covalent bonds.  When these are broken and the proton that once occupied two positions, collapses to one, breaking the bond.  The energy barrier remains as a ‘control’, the enzyme opening a ‘path’ through it. 

Photosynthesis and Metabolism

In photosynthesis O2 is formed as a ‘waste’ or byproduct as plants produce sugars.  The sugars, later, as ‘fuel’, capture O2 in the presence of the appropriate enzymes oxidizing it, reducing it, once again to water and carbon dioxide, CO2.  The sugars must be continuously replaced over time.  The enzymes will switch on and off as need working with regulators and inhibitors.  The necessary presence of O2 in the organism leads to oxidation and damage to other proteins and structures within the organism which must be repaired or replaced, requiring even more energy.  This is all ‘normal’ and must be overcome if the organism is to remain living.

Life on Earth requires that conditions remain within particular very narrow limits in terms of heat, the mix and proportion of atmospheric gases which go to determining those gases dissolved in water and pressure.  Especially important is the range of ambient temperature within which an organism can keep itself in balance, not too warm and not too cold.  Organisms require these ambient environmental conditions.  They cannot maintain their energy flows outside of them for very long though these vary somewhat between species each having evolved under somewhat different temperature ranges.

They do this by having metabolism rates ranging from very slow to much faster than ours, living at different ‘speeds’, requiring more or less fuel.  Trees live at much slower ‘speed’, but they are still alive with energy.  Many cold blood animals may possess the ability to move quickly in short bursts, but their ‘truer’ nature is exhibited in their relative lethargy as they slowly digest their meal.  Remember that digestion is the breaking down of food into useable form, cellular respiration still taking place in each cell much like it happens in plants.  Most species depend directly on their surrounding ambient temperature, their body temps varying directly with their environment which slows or speeds their metabolism. 

Homeothermic, or warm blooded, animals utilize a portion of their own energy to produce body heat utilizing various mechanisms to help them maintain their internal conditions.  Some organisms activities cycle every day in direct response with changing ambient conditions, others do so to a point but then are capable of reducing their metabolism, going in to either torpor, like hummingbirds or hibernating over the course of winter.  Compared to animals plants are slow metabolizers, over a given period of time their cells require less energy to continue on in a living state.  Plants accomplish this by having adopted several strategies more unique to them.

Most plants are anchored in place and are not capable of independent movement.  Movement requires unique physical structures which tend to be more energy intensive.  As poikilothermic organisms, plants rely on ambient conditions to maintain themselves and are unable to either produce heat to warm themselves or perform physical internal functions to cool themselves.  They rely on several different dormancy strategies to slow or shutdown their metabolism when conditions move too far away from their optimum, conserving both their energy and tissues.  Many plants form cells and structures which once formed cease growing, becoming static, like the wood of trees and shrubs.  These tissues no longer require sustenance or regular energy flow.  They do not respire.  Their living tissues tend to live in a ‘shell’ around these static structures.  Plants also tend to produce deterministic growth, tissues that grow to only a certain size, make their energy contribution to the larger plant and then are shed at the ends of their useful lives, like leaves and herbaceous stem tissue.  While animals may produce similar static structures like some mollusks and bivalves do their shells, most animals are comprised wholly of living tissue that must continue to be supplied with nutrients and energy to remain alive.  An organism’s structure is thus an integral part of its living processes, each individual and species unique.

Organisms, while living within a prescribed range of ambient conditions also work to maintain their internal conditions.  Both of these must remain in balance for the organism to continue living.  Traditionally physicists argued that quantum mechanics could not apply in organisms, that they were too wet and warm and that quantum coherence would break down within them due to all of ‘noise’, interference, that takes place inside them.  What they are beginning to find, however, is that this noise, inside a healthy organism may not just cancel itself out, in a way analogous to noise cancelling headphones, but that certain quantum actions may be enhanced by them within a healthy organism.  The intricate dance of life continues, reinforcing itself along the way.

There are several stages of growth among certain species in which this energy and nutrient flow are not necessary and which are in fact more defined by their static metabolisms.  These include seeds, pollen and the spores of particular organisms which are able to arrest their growth until supportive ambient conditions prevail.  These structures possess the capacity to suspend themselves, for periods of time, sometimes almost indefinitely, while still containing the balance of energies internally, that with supportive ambient conditions: water, gases and heat and in some cases light, can be effectively ‘jump started’ into life.  These structures do not require a Frankensteinian spark, but alone, largely powered by the water these structures imbibe which, in its fourth phase, donate positively charged protons which produce internal energy gradients that tip the scale toward the active flow of energy and nutrients through its now able to develop tissues, structures and organs.  Such water, coupled with the necessary proteins that abound in the cell and the energies of light and warmth begin this process which then is capable of the oxidizing carbohydrates and beginning the production of the building blocks, the proteins, enzymes as well as the batteries of ATP.  This initial stage of germination essentially primes the organic engine of life…and it is a process that takes place at the subatomic level, splitting off protons from the water molecule, restructuring it as a denser fluid and creating a charge gradient, a differential which animates living organisms.

Quantum Physics and Biology

Erwin Schrodinger, a pre-eminent theoretical quantum physicist, you all remember the paradox of Schrodinger’s cat, wrote a small book published in 1943 in which he discusses the physics of life, what must be true in its processes, based on what they knew of its observable processes.  They reasoned that organisms, composed as they are of matter, must follow the same chemical and physical laws that hold for all physical matter.  His book, “What is Life?” became a classic which inspired the formation of the science of microbiology and set the stage for the discovery of DNA and its double helix structure in ’53.  Schrodinger began the process of merging the science of biology and quantum physics, two fields previously separated.  Biology, dependent upon the worlds of classical physics and chemistry and keeps running up against problems with the  solutions crafted to fit them, ‘solutions’ that leave lingering questions or doubts, that in short, defied the ‘elegance’ that theoretical physicists strive for.  When science keeps running up against ‘exceptions’ it is a signal that something is wrong with the operational theory, that something essential is being missed.  The synthesis of quantum physics and biology is beginning to provide the elegance and symmetry that science strives for, a logic that tends to work toward the idea that the simplest explanation is the most likely…Occam’s Razor.

Quantum physics, to the layperson, may appear to be working toward the convoluted and complex, but when you can’t ‘see’ something from where you stand, it can require that you change your position, your perception or the ideas that you have based your understanding on, in order to bring it together.

Other quantum biologists are working on understanding other cellular functions, none more important than the accurate reproduction of DNA, something they refer to as fidelity, remaining true.  In reproduction fidelity is essential and it is accepted that more than one ‘copying’ error in a billion in an organism’s DNA, can be fatal.  Organisms routinely do this in the process of reproduction while it is virtually impossible for us to do anything consistently this accurate in any kind of lab or production setting.  What they propose is happening is that during meiosis, when the double helix splits in two, divided at the center of each ‘rung’ in the ladder, the other side is duplicated, built to match.  The base pair are held together by hydrogen bonds, essential each side ‘sharing’ a single proton.  In order to do this the match must be essentially perfect.  This is action at the quantum level not the ‘classical’.  DNA polymerase ‘unzips’ the matching pairs and builds back the other side with the necessary proteins, of which their are only four which must be strung together in perfect order, billions of them.  This DNA is within the nucleus of each of the trillions of cells with the human body, again, every other cellular organism have somewhat more or less than this.  This is a remarkable fete.  Add to this the copies of RNA that is continuously created then transported to the literally thousands of sites with each cell which is used to create every single protein molecule and enzyme used within the cell to build and repair itself while also coordinating all of its functions simultaneously, through out the life of the organism.   Human DNA contain about 3 billion base pair, nucleotides, in the rungs of their DNA ladders.  Other organisms have more or less sometimes significantly more such ‘rungs’.  Each ‘base pair’ is recognized and must be duplicated precisely.  A single error in a billion can potentially result in non-viable offspring or genetic diseases.

Photons strike chloroplasts, releasing ‘excitons’, yes this is what that call them, which ‘quantum walk’ down a pathway to an energy center where they collectively come together working to break the bonds of CO and H2O and form the simple sugar glucose, C6H12O6 and O2.  This quantum walking is something impossible in the world of classical physics.  It allows particles of small enough size and their energies to move across spaces and boundaries in otherwise inexplicable ways.  It reaches back to the ideas of probability of something being in in all possible places at the same time, until it ‘collapses’ into a new and single position, making it ‘real’.  It requires that the stage and conditions be set just right in order for this to happen and, because it does, it speaks to the precision and complexity of this process in photosynthetic plants. 

Scientists are working to produce a quantum computer, a computer which essentially considers all possibilities at the same time, pursuing a question in all directions at once and each one of those in all directions, on and on, following each inquiry simultaneously in an exponentially expanding pattern.  Science is beginning to look at living organisms as a type of organic quantum computer, not the brains of higher organisms, though some are pursuing the ideas of memory, consciousness, creativity, in a similar way, but of the living cells themselves moderating their own conditions, making quantum level adjustments in order to maintain their living state.  If various functions in an organism appear impossible, staying within the limits of the old paradigm, how is it that they happen and that they do so so consistently and elegantly?  Quantum biologists, along with physicist, neurologists and brain specialists are beginning to understand that this ‘impossible’ things happen within organisms, with all of the constraints of their warm mushy bodies, because they are able to ‘see’ their way down these quantum paths, over coming the randomness that would seem must be at work, navigating its way from moment to moment past the over whelming ‘almost’ certainty that something can’t happen, to an every day reality in which it does, smoothly and reliably until it no longer can and that individual dies, falls off of the razor’s edge of dynamic stability, of energetic possibility, into entropic stability.  Quantum physics provides us with an approach to see just what that thing called life is.  It will allow us to pull life out of the realm of religious miracles into the brighter, understood world of wonder and awe, still miraculous, but beyond the world of magic and black boxes, into the known.

All of this and very much more goes on within an organism, within each of its cells, coherently and in a ‘perfectly’ coordinated manner.  Any one of these processes is nearly impossible to duplicate in a modern lab, let alone the thousands of actions taking place within each cell.  Organisms are self-regulating as long as ambient conditions remain within livable parameters.  Coherence happens.  Sub-atomic particles, including Hydrogen ions, protons, behave in a coherent, non-local manner, as if they were directly connected, functioning as one…one might even say ‘purposefully’!  Within organisms, particularly in the sensory arenas and in the ‘communication’ which must and does happen internally, and has now been demonstrated to occur between related organisms, these particles behave in ‘impossible’ ways, they exhibit quantum behaviors, accomplishing what seems impossible to the layperson.  How can something be in two positions at the same time?  How can something ‘materialize’ across impenetrable barriers or overcome impossible energy barriers?  They do this in living organisms.

Prior to the slow adoption of the various theories and maths developed to explain quantum physics, organic chemists and biologists attempted to use accepted classical theory to ‘explain’ the processes and life within the cell and organism.  The ‘story’ they could tell about life was deep and logical.  Science and theory evolve with our abilities to ask and answer questions becoming more refined.  Older theories can later come to be more narrowly defined as is the case with ‘old’ classical physics of Newtonian mechanics and thermodynamics, these still apply, but the cases in which they do and certain exceptions are now more thoroughly deliniated.  The field of biochemistry has been more quick to adopt because the reactions which they study are all chemical and occur at the level of single atoms and molecules where quantum behaviors are widely accepted, though they may be ‘trivial’ or more rarely, but still not unusually, reactions involving quantum coherence, where the magic of ‘superposition’, of particles being in all possible states or conditions at the same time. 

Biology has been much slower to adopt this, in large part because to be expert in either field requires years of focus and Quantum Physics is a very technical and non-intuitive field that seems to clash with direct experience as I discussed above.  Integrating the two requires a thorough understanding of different fields and doing so sets you up to being criticized from both sides.  Quantum biologists agree with their physicist fellows today in that living organisms cannot be excluded from the hard science of physics, that laws are applicable to both inert objects and organisms.  The problem lies in understanding how.  Physicists have studied this in the very controlled environment of the lab and the particle accelerator as well as theoretically and mathematically.  The warm squishy world of living organisms has in earlier decades posed an impossible barrier to their thinking, but as I suggest above, current research is beginning to offer ideas as to how it can be.

As It Was: Evolution and Setting the Stage for Life

As it was, life happened here on Earth, beginning under conditions that would be toxic to Eukaryotic life today and the higher organisms that sprang from it more than a billion years later, which helped modify those very conditions into what we have today with an oxygenated atmosphere and a band of climatic conditions that support it, an oxygenated world that itself would have been toxic to the earlier anaerobic world.

Big Sagebrush, an ever-gray woody shrub, follows a path it shares with other sclerophyllous plants, allowing itself to conserve its above ground tissues despite drought, intense summer temperatures and relatively severe freezing winter temperatures. Sagebrush, one of several Artemisia species, are relatively common across the Intermountain West and Great Basin regions.

A native thistle in eastern Oregon blooming in late May, a herbaceous perennial attuned to the arid harsh conditions. Dormancy enables organisms to survive and flourish in otherwise hostile environments, keeping their ‘spark’ ‘smoldering’ until conditions are more conducive to active growth.

Arid cllmates, like that of the lower Deschutes River, support spring flowering, taking advantage of soil moisture that declines quickly as the summer season takes hold, encouraging plants with triggers and thresholds that allow them to respond to these patterns, conserving their living tissues while responding to appropriate cues in order to replenish themselves when they can.  The evergreens of these protect their tissues with sugars

Broomrape, one of those parasitic plants that seem to defy many people’s expectations of what a plant is, having neither leaves nor chlorophyll to photosynthesize carbohydrates with, but still producing flowers and seeds to reproduce, drawing on the carbohydrates from a nearby photosynthesizing plant for its carbohydrates as an energy supply. Species of ‘hemi-parasitic’ plants have a more conventional root system that is able to draw on the soil for some part of its needs, but all plants still produce the metabolites they require to meet their own growth and maintenance needs.

This graphic shows a timeline for Earth showing certain select events took place. The age of these is indicate in Ma, millions of years ago. The formation of the planet itself from debris orbiting the sun consolidating some 4,550 million or 4.55 billion years ago. From Wikipedia

The Big Bang happened some 13.8 billion years ago.  Earth formed with our solar system some 4.5 billion years ago.  The elements within the universe formed over time with the Bang rapidly with its expansion and over time within the stars that have coalesced, burned out and continue today.  Arguably another billion more passed on Earth before the first appearance of life here along with some early form of photosynthesis, bacterial…it did not produce sugars and O2.  O2 was actually toxic to the anaerobic organisms that existed in its waters and the atmosphere was without significant amounts of it.
 The capacity for life required the passage of time while matter, its molecules and the physical structure of Earth and its conditions evolved.  The availability of CHNOPS, the essential six, carbon, hydrogen, nitrogen oxygen, phosphorous and sulfur, did not immediately lead to the formation of the 20 amino acids which, mixed in various combinations, comprise the long chain molecules of the proteins essential to the structure of virtually every organism.  Nor did the availability of phosphorous in its form as phosphate immediately lead to the formation of ATP, Adenosine Triphosphate, the organic ‘battery’ that powers many metabolic processes that take place in all organisms.  These complexities, these possibilities, were built over time through the duality of sub-atomic particles, their quantum dance, simple and more complex chemical reactions, the building of organic compounds produced by the simplest organism through the most complex today, each playing an essential role.   Everything, literally, every organism exists only as member of the much larger Earth community.

Organic chemistry teaches us that life is composed of carbon, oxygen, hydrogen and nitrogen, there are many other elements necessary for it in more minor and trace, quantities, that give organisms particular capacities. But life is not a simple recipe of ingredients, add and shake.  Calcium, sodium, phosphorous, iron, magnesium, zinc and others are all utilized to varying degrees…and everyone of these, must be in an appropriate proportion and form, or be capable of being transformed into such a form, by the organism or supporting processes in the soil, by bacteria, before it can be utilized, within its structure and metabolic functions, informed, its energies, its ‘harmonics’ tuned to be compatible, in order to take on a supportive role within the organism. 

Biology teaches us that any organism is a product of another.  Life comes from life.   DNA placed in an environment of the perfect blend of chemicals, held at the ideal temperature, will not yield any organism.  It requires the animating and organizational power of a particular and living organism.  Self-organizing.  Self-replicating.  Self-maintaining.  Some argue that life is a direct extension and manifestation of this universe, an expression of it, not random at all, that life is moving toward something, that life is a state of ‘becoming’, building on what has come before, in which successful patterns effectively resonate within a field, exerting morphogenetic effects, shaping and shaped by, every individual.  The idea of such a morphogenetic resonance is much more controversial, but it has its proponents amongst select biologists and physicists.  Quantum physics and its theoretical practitioners have demonstrated time and again that there is much more at play in the universe than we can perceive.

In all cases an organism behaves conservatively, to maintain its state of health, succumbing when it is no longer able to do this, when it begins to lose its integrity as an organism, succumbing to threats posed by conflicting energies of physical and oxidative processes and organisms it comes in contact with.

A Diamond Back Rattlesnake we met on the trail in Central Oregon, still too young to have any rattles, coiled amongst dropped Ponderosa Pine needles.  As different as their structures may be they still share an amazing amount of patterns at a cellular level.  While the ‘hard’ structure of the needles remain, the live cellular tissues are degraded and desiccated.  They cannot be resuscitated.  Their trees have sacrificed them, actively, having formed an abscission layer between the tree’s permanent vascular structures and the fascicles, the bundled structure binding the individual needles together.  Leaves are all limited life structures that plants commit limited resources to. When their life span is over or their useful capacities are compromised, they are sacrificed.  Most animals, like this Rattle Snake, are more invested in the longevity and health of their own tissues and have evolved strategies to sustain them over the longer term, replacing whole cells or replenishing individual proteins within them.  More complex animals do still shed or sacrifice cells, especially those protective tissues, such as skin, scales, hair and feathers in addition to those lining their digestive and respiratory tracts.  Plants do this as well continuously shedding and replacing hair roots as they ‘search out’ water and nutrients.  Patterns are shared as are strategies. In case you were wondering the wedge shaped heads of vipers, the broad base where their lower jaw attaches, house their venom sacks. The snakes can control the amount of venom they release, delivering a ‘dry bite’ if they have no intention of trying to consume their target as prey, increasing the amount when prey is larger. Once spent the venom takes time to replenish and is therefore ‘valuable’. The delivered venom helps with the snakes later digestion of the prey as it begins to break the target’s proteins and tissues down as their hearts continue to pump it, with their blood, throughout their bodies.  The poison takes some time before the prey dies and the snakes are required to follow after.  This affords the snakes some degree of safety if the prey is itself dangerous.  Younger vipers, like this Rattler lack the experience to know this and may inject too much poison. Additionally, their lack of rattles makes them more dangerous as humans may unwittingly stumble into them. Don’t count on a ‘dry bite’ from either an adult or juvenile Rattler!

The structures of living organisms are very particular and share many patterns, if not most of them, with one another.  Nothing succeeds like success.  These patterns can repeat even when lines of genetic inheritance have veered widely apart over the course of millions of years.  The patterns and genetics are much deeper, much longer than we can grasp.  Successful patterns tend to be self-reinforcing and are self-replicating or reproducing.  While they may not be identical they stay within a proven range.  Patterns in the non-living world tend to be simpler, more stable, less dynamic without the internal energy flow of life.

Before science ‘we’ studied ‘natural history’, the story of the living world around us.  The practice of science has come relatively recently to us with its structured and logical methods.  For much of our time with science its been believed and taught that all things tended toward entropy, a neutral state of energy, higher energies dissipating in the ‘direction’ of lesser energies, its stores spent, the universe winding down to a cold, dead, thing, but this was before our more complete understanding of the quantum world and the tremendous energies contained within matter and the idea that matter at its core, is energy, before our more developed idea of evolution and the understanding of the universe’s tendency toward biological complexity and the evolution of form, increasing the complexity of life.  Biology and life are in fact additive in their effect.  While it is true that life does consume and ‘spend’ itself, it does this in order to live and over time the organisms and the systems that support them, are driven to grow, increase and diversify, to improve!  Prior to this we focused on entropy, the negative, aspect, useable energy spent, life winding down and death.  This is understandable with so much of western philosophy being centered on the individual, our lives, our souls and fate.  To do otherwise requires a more wholistic view and assigns oneself a less central, but necessary role.  Without this countering and ultimately predominate ‘force’, life would never have developed, never been capable of ‘responding’ to the changing conditions on Earth, the several extinction events that have occurred….Under ‘entropic thinking’ the only ‘explanation’ left to us was some kind of singular, god level, creation event, from which we are winding down.  Entropy is not the whole picture.

Over Earth’s several billion years life has evolved in increasingly more complex forms.  This is undeniable and has been demonstrably proven.  These same energies part and parcel to even the smallest, most basic particles and strings, that comprise everything in the universe, contain a self-organizing principle which pushes it in the direction of both stability and complexity, towards an evolving life.  This self-organizing principle has manifested itself in multiple ways, an important one of which, is the ability of an organism to function as a kind of quantum computer, giving it the capacity to maintain the precise conditions needed within its ‘noisy’, warm, wet interior without which these conditions would consistently result in the decoherence of quantum behavior, stopping, the every day ‘miraculousness’ that occurs continuously within organisms, central to their metabolic processes and stymieing its abilities to process its sensing and responses, this without broaching the topic of awareness and consciousness. This is no small thing. 

A survey of Earth’s evolution further demonstrates this.  Stability is insufficient on its own.  A stable universe is static, unchanging, or in decline if not ‘dead’….The fact of ongoing evolution demonstrates that it is generative, not merely maintaining itself.  In a ‘living world’ individuals exist at all stage, some are ‘winding’ down while others are beginning, reset, spinning up, developing in relationship ‘with’ under dynamic conditions!  Each individual follows the path particular to its own reproductive cycle.  The probability of evolution is integral to matter and the universe.  So, life evolved and continues to do so, moving simultaneously toward increasing stability and complexity, with a higher demand for more complex energy throughput, as it always has done.   Life in fact ‘had’ to evolve.  This imperative is seated within the very nature of matter.  Life’s apparent rarity throughout the known universe is due to the relative rarity of ‘materials’ while the supportive conditions themselves are spread across the vast expanses of the universe, not the absence of some singular and precipitating creative ‘event’. 

There are four universal forces that underlie all of matter and its ‘behavior’: gravity, the electro-magnetic and both the strong and weak nuclear forces.  Gravity works to draw matter together building bulky mass, undifferentiated.  The electromagnetic forces both tend to attract and repel in a more organized manner while the strong and weak nuclear forces speak to the stability of atoms themselves their ability to interact and react forming new atoms and compounds.  The statement that ‘Nature abhors a vacuum’ is not exactly true.  Deep space is not filling with matter.  Matter does not spread itself out at like density across the universe, only where there is a sufficient energy difference, a ‘gradient’, between two adjacent spaces will matter move to equalize it, moving from higher to lower.  A vacuum, in the classical sense, is an absence of matter in any form, which nature will certainly fill, ‘if’ it can given the conditions in effect there.  Not all space can ever become suitable for life.  Life will propagate and expand to fill those spaces supportive of it, while also ‘working’ to ‘improve’ and expand those conditions within relatively narrow limits.  Nature will work toward evolving the conditions and constituent parts of that space as it can.  But, again, that capacity is limited by the several forces that effect matter and matter’s availability.  Electromagnetic energy, in the form of light, is an essential factor.

Matter itself aggregates, coalesces, through gravitational, electromagnetic and the large and small nuclear forces that effect all things, drawing gases and inorganic minerals together, creating settings, opportunities for life.  Not all planets possess the physical and energy characteristics that are supportive of life, very few do and most never will.  Other forces are at play in the universe guiding its development, classical forces that work toward their own ends.  Life is a layer of possibility on top of the classical forces so important to shaping the universe.  Not all of space could ever be filled with living organisms.  The universe could not sustain it.  The living cannot exist without stars and the availability of non-living matter.  Where conditions are amenable to life’s beginnings, ‘it’ will work to evolve the conditions and create the organic molecules that are the precursors to life.  However, most planets will simply be too remote from large enough and stable enough energy sources, stars, or themselves be too small to possess the gravity necessary to retain the gases life as we now know it requires.  In other cases planets can be too massive and possess a force of gravity that would crush an organism, whose ‘air’ itself would possess a density and composition that would be toxic to life.  Life will arise where it can.

Bacteria, Archaea, the Prokaryotes, the simplest single-celled organisms, arguably the oldest and most basic forms of life, are still here today, still playing a necessary role as essential members of the larger living community.  Together with the more recent and complex Eukaryotes, cells that comprise all of the plants, fungi and animals of today’s world, they fill the innumerable niches in the world.  Numerically, prokaryotes form the vast majority of living organisms. They persist because of their stability as species and abilities to adapt to changing conditions within the basic pattern of their structures as species, not individuals.  They play essential supporting roles in balancing the conditions within which all organisms live.  Individual organisms will always come and go, but the species and their many populations, persist.  In a healthy world the extirpation of local populations and wholesale extinctions are rarities.  They consume and oxidize organic, carbon based, and inorganic substances, often rendering the toxic, non-toxic, they perform essential biochemical functions within multicellular organisms, often serving essential roles in the digestion of foods other organisms consume…they are not just the source of disease and decay, though they can play roles in those as well.   

Anyone individual organism possesses a degree of fragility, of instability.  The  same generative force that drives us toward evolution, brings with it the necessity of death, as a balancing principle.   Individuals are not intended to live indefinitely…they wind down, age and die making ‘room’ for the next generation, the next round of innovation.  Survival’s goal will never be of some particular individual, nor will it be of any given species…that is a bias in our thinking.  Species without our level of awareness, consciousness or sense of self, do not make this mistake.  Higher, more complex species, have come and gone and seem to be doing this on an ever shorter cycle, as this particular living ‘thread’ plays itself out.  Complexity increases, structures become more specialized, focusing the energetics of basic matter, within their structures which at the same time press us forward, alive, animating, directed, highly structured in both individual terms, but also in ‘community’ terms.  Life is this walking along the edge, balanced between being and non-being, our physical selves, ‘momentary’ vessels carrying the energy of life, just as do those of any other organism, literally held in the balance, living within the limits of the structures we ‘inhabit’, falling out of them, when we stray too far exceeding the limits of our finite selves, before we are ‘called’ back into the process to try again….Life possesses a ‘direction’, one that, because we are a part of the process, we cannot fully understand.  Life and our lives are not the vessels that contain it, but the energy that animates us all.  In this we are similar to any matter, all of which is highly structured, informed, energy.  As individuals and species we must trust in this, in order to perform our roles as an organism to the best of our abilities and then demonstrate our willingness to surrender to make way for those and that which comes next, graciously and because we are humans, as elegantly as possible.  We are much more than ‘animals’ in the pejorative sense that so many people throw around today.  We are ‘of’ the universe, though we have largely estranged ourselves from it.  

We are called to remember that life is not some endpoint, but a path, a process and we will never know its end point, we are simply incapable of understanding a process so much bigger and older than we are.  This animating energy that manifests within living organisms springs from the very nature of matter itself at its most basic form.  In a sense we are the music, translated into life by the dynamic and unique structures of our bodies, by the compounds and particles that comprise them, tuned and orchestrated, structured and informed, integrated ‘wholes’ of the processes and forces at work across the universe.  We are here to play our part, to sing our song, in a very literal sense, as the larger process of evolution and life plays out.  Knowing this should be sufficient.


Suggested Reading for the Reader With Limited Physics Background

To understand the world you have to have some idea of the working theories of the day.  Quantum physics is a difficult topic because it is so foreign to our direct experience, it is transforming our understanding of biology and the other life sciences.  What science is finding today is that direct experience has been preventing us from understanding what is going on behind the world’s ‘curtain’.  Understanding does not remove our sense of awe and wonder from the world, it does not diminish our experience of its very miraculousness, it enhances it and deepens our relationship with the world around us.  Be brave readers!  Dare to learn! 

The following are books for the interested layperson.  They attempt to bridge the gap in understanding we have without going over heavy into the rarified worlds of mathematics.  These authors are attempting to do that.  If they are too much, libraries stock other titles that are simpler introductions.  The goal is to understand the larger concepts and build from them.  Stephen Hawking was a big challenge to me when I first read his books and I struggled.  None of these are light reads, but be easy on yourselves, read them for their larger ideas.  No one would ever sit and read a book on the Russian language and expect to walk away from it fluent after one go through.  Though these are in english, they are ‘foreign’ languages just the same.  We’ve spent our life times learning our particular world views and we can’t change them with a flip of a switch or a page.  Over time, with familiarity, their subject will reveal itself.  Look into more traditional books on botany, cell biology, evolution and genetics.  Grow and observe plants in your garden to help anchor the theoretical to your own experience.  There is no reason these topics should remain opaque to us and much is to be gained in their understanding.  Don’t feel limited to these titles, there are many more accessible books out there coming at the topic from ‘different angles’.

Stephen Hawking, “A Brief History of Time”, Bantam, tenth anniversary ed., 1998.
Brian Greene, “The Elegant Universe: Superstrings, Hidden Dimensions, and the Quest for the Ultimate Theory”, Vintage, 2000.
Gerald Pollack, “The Fourth Phase of Water: Beyond Solid, Liquid, and Vapor”, Ebner and Sons, 2013
Johnjoe McFadden and Jim Al-Khalili, “Life on the Edge: The Coming of Age of Quantum Biology”, Broadway Books, 2014
Mae-Wan Ho, “The Rainbow and the Worm”, World Scientific Publishing, 2008
Nick Lane, “The Vital Question: Energy, Evolution and the Origins of Complex Life”, W.W. Norton, 2015.
Erwin Schrodinger, “What is Life? with Mind and Matter and Autobiographical Sketches”, Cambridge University Press, Canto ed., 2006


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