Physics, Evolution, Natural Selection and the Generative Power of the of Far Out of Equilibrium Dissipative Structures (Organisms), part 2

Chemists have often argued that everything is chemistry and if you don’t know about it, what can you really know of the world? A current Periodic Table, one with considerably more elements than were contained in the table from my high school chemistry days, this one including many of those transient elements created in particle accelerators. These ‘new’ elements are very unstable and breakdown rapidly. Some are thought to have existed only at the beginnings of the universe…sometimes in its first moments or during vanishingly rare exceptions. I know, this is very ‘nerdy’, but I go to the interactive table on the linked site frequently to learn about the particularities of elements of interest to me. That table responds to your questions about changing ambient conditions and their physical ‘behaviors’ and capacities for particular reactions. Check it out.

On Pattern, Chemistry and Life

Pattern builds upon pattern.  Whatever you start with effects and limits everything that follows whether we are talking about masonry bricks and stone or Eukaryotic cells and organic molecules.  A different starting point or ‘decision’ at any point in the process, effects every ‘decision’, or even possibility, there after, effects the likelihood of what is to follow, shapes the possibilities, the future, through the evolutionary process…but does not determine it.  To speculate whether other amino acid groups are theoretically possible does nothing to change the course we are on.  The capacities and characteristics of your most basic components set the stage for all that follows, the brick analogy only takes you so far.  Bricks, no matter what you do with them, are very limited in what they can create…how they will ‘behave’ when structured as a wall.  They do not, when combined into a structure, acquire properties that no single brick had before their assembly…their futures were ‘decided’ the moment they were made into bricks.  They remain bricks.

The elementary particles, the several types of quarks, leptons, bosons, etc. all have very specific properties of mass, charge, magnetic moment etc. which are the basis for the properties of all materials.  Subatomic particles, these supremely tiny constituent parts, the quanta, that comprise everything we can sense in this universe, have, in contrast, vastly wide potential, transforming as they combine, becoming new ‘things’.  They possess energies, interactive capacities, that when correctly configured, are transformative.  The whole can be greater than the sum of its parts.  One might think that with them, all things are possible, at least until irreversible combinations are made.  Every ‘structure’ possesses inherent qualities and carry with them limits that will make successive structures and events more or less likely.  But there are other ‘things’ in this universe that we can not sense, cannot perceive, not directly anyway, even with the aid of advanced technologies, but we ‘know’ exist, because of the way the universe ‘behaves’. 

There is as yet no ‘complementary’ Periodic Table which includes and defines the still poorly understood ‘substances’ of ‘dark matter’ and the ‘dark energies’ which together, according to some physicists, comprise 95% of the universe and remain undetectable to us today.  Such matter and energies fill ’empty space’.  We still know so little of existence.  Our ignorance will continue until we are capable of more directly detecting the ‘dark’ stuff of the universe.  Elements and molecules, the universe itself, is not limited to what we know and can ‘prove’.  We do not have to understand something for it to exist.  Nor is belief alone enough to brings something into existence, but when belief aligns with reality it becomes very powerful.  Belief can greatly assist in the unfolding of a probabilistic universe…but, first we have to see the patterns which exist and have an understanding of life, its prerequisites, its limits and parameters, the relationships within which it exists, so we can prepare the way, become a bridge for the unfolding. We do know that there is more ‘there’ than we can explain, though the ways in which it comes into being are not clear to us.  We postulate and hypothesize, note the ‘holes’ in our understanding, the ‘conflicts between the world we observe and the shortcomings of our ‘explanations’.  We seek knowledge, congruence, to be atuned and in tune with the life around us, because we possess the capacity to be an active part of evolution, its active, ongoing advancement into complexity, diversity and beauty, not simply consumptive, a brief ‘correction’ in life’s time line…here then gone. 

Take a molecule of hydrogen, H2 , formed from the most common element, by far, in the universe, and one of oxygen, 02, (both of these in their gaseous form exists as two atom molecules, singularly they are much less stable.  They have an affinity for each other.)  In their gaseous state, combine them at room temperature, add a ‘spark’ to initiate the reaction and the hydrogen ‘burns’, combines with the oxygen, ‘oxidizing’.  By doing this you have liquid water with an array of capacities that stagger the imagination, capacities that water’s base elements would not seem to even suggest.  What’s more, when these bond to form water, energy is released in the form of heat and free electrons.  This heat can potentially drive a continuing reaction, the positively charged hydrogen ions, having ‘lost’ their negatively charged electrons in the process of bonding, linked strongly to the two available ‘spaces’ in the the oxygen’s outer shell, transforming it radically.  The now free electrons are available to drive other reactions.  (This is the source of electrical power technology is still trying to effectively harness in the hydrogen fuel cell.)   

Take one of those hydrogen and bond it to a single chlorine atom and you have one of the most potent acids found on the planet, hydrochloric acid, HCL, an essential component of digestion, making it possible for animals to breakdown proteins in their food into parts which can be reconstructed into the proteins an organism requires for its own growth and ‘maintenance’.  Every atom, every element has been placed on the Periodic Table according to its precise attributes.  One cannot randomly combine them to create one’s own molecules…the selected atoms have very particular compatibilities…affinities.  In this universe certain combinations are more likely, more probable, than others, and there occurrence reflects that. Every such possible combination produces a molecule with its own particular signature, one that is not simply additive, but like so many things, if one studies it, have characteristics which are predictable, others perhaps less so.

Each element has particular characteristics which are modified when they bond to other atoms and molecules.  Once having done so they can ‘behave’ very differently.  These molecules themselves are more or less stable and can, under the proper conditions be switched back and forth, bonds broken and reformed resulting in a release or absorption of energy through chemical reactions.  There are various types of bonds.  Those that hold an atom’s nucleus together are far more stable than those between atoms and molecules.  Some materials are incredibly stable, their molecules more or less locked in crystal structures, while others are more transitory capable of breaking down as conditions change such as temperature and pressure.  A relative few atoms can degrade over time predictably releasing energy in the form of radiation, heat or light as their internal, nuclear, bonds are ‘broken’.  All elements exist in a solid, liquid or gaseous state which change when particular critical threshold conditions are met.  When these change it is termed a phase shift, going from solid to liquid, liquid to gas and back. In liquid and gaseous states elements and molecules move in more randomized, freer, movement, the bonds between individual atoms and molecules themselves weaker and more transitory. They possess higher levels of kinetic energy, of movement, in response to their temperature and the pressures upon them, each atom moving with higher velocity,  ‘passing’ molecule to molecule more freely, more independently of one another.  When ‘cooled’ to a particular temperature, they ‘shift’ to solid, and to our perceptions, appear fixed, dense, impenetrable, unless physical broken.  On Earth within the temperature range that exist across it’s surface and ‘crust’, much of matter has cooled and congealed often forming mineral crystals, while water balances uniquely in the middle shifting between phases with the normal range of our temperatures, that dissolved within them and, as it turns out, in specific cases, the molecules they reside next to.

In more unusual, special cases, matter can exist in a liquid crystalline form, like molecules bonded in two dimensional sheets, but moving more freely in the third dimension, as if each ‘sheet’ were sliding passed the others, giving such materials unique properties.  Water, one of the most important molecules in every organism, is one such molecule that does this, forms a ‘fourth’ state, capable of realigning itself under certain conditions in the presence of hydrophyllic, water ‘loving’ vs. hydrophobic, water repelling, protein molecules and like charged gels.  Researcher Gerald Pollock and his team have described what they term ‘Exclusion Zones’ or EZ water, which is molecularly different, giving it capacities one would not expect from ‘normal’ bulk water…and these characteristics make possible many of the functions and actions essential within cells and organisms. 

Proteins, the peptide chains that comprise them and the amino acids that form these, are among other such essential molecules to life, both requisite and products of, living organisms.  These have particular structures linked directly to their functions, structures built upon basic patterns, with very small modifications, which have been on Earth for billions of years.  These possibilities, inherent to matter, are essential for life…as well as being products of it.

Molecular structures are extremely small and are unobservable with even the most powerful optical microscopes, yet they combine to form precise physical patterns.  These structures, these molecules, form living cells and everything else in our world, which when large enough, we can perceive and then recognize, so that we can classify the tissues and organisms of which they are a part, while their functional patterns determine the processes that occur inside cells and organs which support the organisms we see.  It is a bit of a truism, but organisms are what they are…because, they are what they are. 

More recent studies have shown that a single simple cell may contain 42 million or more protein molecules, which are themselves ‘giants’ in the molecular world.  Each cell contains even more water molecules, lipids, calcium ions, ‘free’ protons and electrons…all of the other essential compounds and ions, in a liquid matrix, flowing within and between each cell. The smaller patterns, the physical structures of the proteins and cell structure, shape the cellular world within each cell’s membrane, and greatly effect what these similar looking structures can do.  In multi-celled organisms such as all higher plants and us, they all form a whole, interconnected and dependent.  These patterns are ‘duplicated’ within every organism, ‘assembled’ into complex structures, structures which play a direct role in what is and can be possible as the process continues on.  Within each cell the chemical ‘soup’ of its protoplasm, works in a coherent and complex way to sustain the life of the cell and larger organism.  It is a physical, chemical, energetic and structural process.  Whether within a cell, a lab or in the works of an industrial process, chemistry occurs, facilitated and guided by all of the supportive combined structures and processes.  Chemistry happens…not just the limited, controlled experiments of laboratory scientists, but the everyday, complex interactions of nature and life. 

Within an organism the limits and controls, the activators and inhibitors would seem to be free and even magical, but it is a highly integrated, patterned and self reinforcing process…coherent.  Chemists have run uncounted experiments of different chemical reactions within matrices under controlled conditions and watched as reactions occur within them, patterned reactions with rates subject to conditions operating on them.  Chemical reactions beginning ‘locally’ around catalysts, spreading through the matrix predictably, sometimes pulsing in waves radiating out, chemical bonds being made then broken, responding to both of the activators and inhibitors which are part of the reaction themselves, relatively ‘simple’ exercises in comparison to the complex chemical soup within cells, where they are auto-catalytic and self-regulating.  The level of sophistication and coordination is staggering in their capacities…within a single cell.  In larger multi-celled organisms the communication extends between cells, coordinating tissue and organ function and in us, culminating in language and our problem solving and creative capacity, perhaps the most astounding such manifestations of life.  Life does not simply happen.  The recipe is not easily tweaked and redirected to create organisms and products far from that created within the processes of evolution.  Scientists’s are very careful to not ask too much of a given process.  They study it for patterns and similarities and, like in nature, seek to tweak it to ‘improve’ its process or to ‘propose’ a possible new line.  Then it is up to ‘nature’ to test it’s fitness, whether it ‘works’.  The impossible will remain out of reach.  What something ‘is’, transforms at each added layer of complexity, every change…it is biological, alive, not the far more limited creation of an industrial process or that set up in a lab.

Science studies nature.  it seeks to understand what is behind the complex patterns that determine our own and other’s lives, how these are coordinated and to what end.  At times science may seem ‘Frankensteinian’ when it attempts what is beyond its understanding.  That is not to say that such an act may always be impossible, but our knowledge at any given moment is incomplete, both in its details and its role in the universe.  We state a hypothesis, we presume and we thus set ourselves up for learning, for success or failure.  Because what we ‘know’ at anyone time is limited, our ability to understand the world that we see is as well.  Our knowledge, and lack there of, ‘shapes’ what is even possible for us to ‘see’.  Knowledge, like organisms themselves, is dependent on what it already contains.  What we can potentially learn/know is limited by what we already do.  In its quest, science fails constantly, but without such attempts, nothing is learned.

We can study the process of photosynthesis or glycolysis, the conversion of sugars to forms useable by the cell, or any metabolic process in an organism and come to be able to describe it in great detail, its redundancies, the delicate balance between activators and inhibitors, the operating parameters of a specific function, as a cell produces more enzyme to smooth the way to a particular reaction in a long line of reactions to meet the cell’s and the larger organism’s ‘needs’.  At the same time, through the production and use of hormones to slow or speed a reaction, the larger organism finds a narrow balance at which it can continue to exist in a more or less steady, dynamic state. 

During the development of the embryonic stage of an organism and its maturation and growth to adulthood, development is much more complex, there are longer, critical cycles that must occur precisely to assure the healthy development of any organism…not all tissues, not all organs are required in steady numbers…an organism develops in stages.  Precise stages…the production of one compound or another, the growth of one cell or another, favored or suppressed, so that whatever is needed, is favored.  All along an overall balance is maintained, tissues or organs developed as needed.  But how all of this works remains elusive. 

Our human optic nerve does not grow slowly and steadily from conception, nor does it continue after it is fully developed.  It awaits its cue and then stops once developed to a particular stage.  The structures within organisms develop at very specific locations within them, the organism following a pattern, much as the branching or leaves forming on a stem in a pattern described by the Fibonacci series, the individual florets of a Sunflower forming in the larger inflorescence, elegant, predictable and satisfying.  The incredibly complex choreography of internal functions within any organism remains beyond us.  We see it, can measure it, follow its various steps, but really have no understanding of how it all actually works, the communication and coordination.  We can see the spatial, temporal and spatiotemporal patterns, the pulses, and cycles, long and short, the precise microscopic and larger structures entailed, and we can know that this is all driven by a flow of energy in a resonate, harmonic manner, but the core, the how and why behind these patterns eludes us.  The patterns are, however, there and we would be foolish to ignore them.

The smaller patterns of any organism building up from organic molecules into a fully functioning being have all of its ‘bricks’ precisely coded in their DNA, those essential building blocks absolutely critical to every stage of development from the embryo onward.  (Some, like Rupert Sheldrake, hold that in a very real sense the universe has a ‘memory’ of these patterns, habits of function, mass and structure, that overlay an organism’s DNA, its proteins, structures and organisms, which resonate within them, which manifest in particular individuals and are heritable, passed from one generation to the next.  The larger patterns, the symmetries and fractal structures that underlie them, would seem to be inherent in matter itself.  Simple mineral structures, the large physiographic structures of mountains and coastlines, all follow from the capacities inherent in matter down to their tiniest parts.  The patterns they form have a rightness to us when we observe them.  They resonate inside us when we see them or disturb us when they are ‘wrong’.  We are creatures ourselves of pattern and are driven to identify them for reasons of survival, wonder and curiosity.  That we may be ignorant of these possibilities and patterns does not change them, but such ignorance undermines our capacity to understand and appreciate them.  That we seek to attribute so much of this to a god, our curiosity and sense of awe at nature’s complexity and inherent beauty, speaks more to habit or a learned laziness than it does to rightness.

Entropy: the Flow of Energy and its Inevitable Decay

Central to our understanding of life is the concept of ’entropy’.  I learned in high school, that entropy is the inevitable degrading of energy to inaccessible randomized motion, heat.  Eventually, we were taught, everything will contain the same amount of energy, be the same temperature, resulting in the so called ‘heat death’ of the universe.  At some date, far in the future, all available fuel and energies will be consumed, lost to low grade heat, and rendered unusable.  All systems would inevitably work themselves down to a state in which there is no available energy left. The universe, would be dead, with nothing left to power its processes…its fuels spent.  This is no longer so clear….

At 13.8 billion years old the universe still has a very long way to go.  For many this set ‘man’ up in a superior position, because it is ‘man’ with the energy and capacity to lift his world out of the muck, to free it from its path toward dissolution, to save it, give it purpose via our ‘superior’ intellect’.  We were, after all the greatest of beings, serving at the right hand of God.  With that belief we have prepared the path to hubris and decline.  Survival and salvation lies within our own hands.  And so, we turned away from the miracle of nature, the imperfect creation of a perfect God, our ‘proving ground’ and in our arrogance claim to lift it up to the heights worthy of our god.  But that’s not the full or correct story of  ‘entropy’.  Such an understanding perverts our relationship with nature and the god we claim. 

Any physical system has a natural state in which it is at ‘rest’, an ‘engine’ still, at ambient temperature, at equilibrium, quiet and unproductive.  At ‘rest’ systems are stable.  Many systems remain in an equilibrium state even as they receive energy quietly radiating away any excess energy.  They exhibit no fundamental change in structure and dynamics.  Other systems, when ‘driven’ with the right form and amount of energy, ‘spin up’, shift phase to a different state with different dynamics, their structures themselves changing in a predictable way and then, later, when no longer able, due to either a loss of available energy or their structures having had degraded to the point at which they can no longer continue, spin back down to a stable state, losing structure.  Organisms, as systems, exist as far out of equilibrium, out of balance, structures and require a continuous energy input to maintain themselves or they too ‘fall’ into stasis.  While their metabolisms can slow, their energy requirement decreasing with it, they can only do so within limits…they cannot stop and restart.  Other out of equilibrium systems exist on a continuum closer to stability and can be far less complex and, not being alive, shift back and forth from one state to another in response to the energies that flow through them.  Living organisms,  are capable of sustaining themselves for various periods of time, as long as their energy requirement is met and a constant flow of energy is available to maintain their out of equilibrium state, a state, in a continuing, though fragile, dynamic balance.  This energy flows through them, degrades in the process, becoming less available as it increases in entropy, that state of ultimate unavailability.

In simple, open systems, such as a limited volume of gases, which are constituted by many trillions of gas molecules, equilibrium is a randomized state, energy is dispersed evenly throughout the system within those molecules. There is no recognizable physical flow from areas of high concentration to low. No ‘region’ that becomes less energized than others. All are at the same energetic level so movement is entirely random. Unstructured.  Disorganized.  No ‘work’ can be extracted from such movement.  But this is an abstraction, a state created and tested in a laboratory.  The real world rarely fits into this limited controlled world.  The real world is dynamic and in constant flux.  Energy is being added and lost.  As higher states of energy interact with matter, with systems, it does so as it degrades moving to randomized heat.  We recognize this process as entropy.  When thinking of entropy we must look at a system in a statistical manner, which is really the only way that we can, because in any system with millions of billions even countless trillions of parts, and beyond to those with truly stupifyingly unimaginable numbers, this is our only practical option.  What is the condition of such a system most of the time?  When we ‘measure’ such systems we are really taking a kind of gross average and averages tend to settle within a narrow range with relatively few molecules moving at rates significantly above or below that…or concentrated in one area more than any other.  Such a system can have countless billions of possible arrangements anyone of which will exhibit the same general outward characteristics, even though the specific locations of given molecules are unique…that won’t matter.  The system will behave in a predictable way.  What matters is the overall outcome.  Reality becomes a question of probability, of likelihood.  Quantum physics has taught us this.  As individuals we see the world in aggregate.  What goes on below the level of our perception is mind boggling…yet it doesn’t make it any less real.  So what is entropy? 

Low energy systems have high entropy, lack much organization, are highly randomized and have a high  probability of occurrence.  These are the most ‘likely’ state.  Pushing such a system into a more structured, organized one, is far less probable and requires an expenditure of energy, it is not the system’s resting state.  Think of a long sandy beach each wave washing up and back, rearranging the particles of sand that make up the beach you see, but it is and always will be, a sandy beach, its form and surface predictable and familiar and in that way the same.  But on that beach build a nuanced sculpture of fantastic character and the beach is transformed, at least for that time before the next high tide. Or, look at a the level of each grain and the configurations wrought by each wave, each is different from everyone that preceded it.  We see, only the larger pattern and, blend these into an average which we recognize as, ‘beach’.  An organism has very low entropy, its particles and structures, at every scale, are highly organized, arrangements, ‘sculpted’ with ‘skill’ and ‘purpose’ into something entirely unexpected.  Such a structure is extremely transient and like other such structures will disappear in time.  All systems tend toward randomization and high entropy.  These forces can only be countered by a continuous inflow of higher quality energy and an outflow of waste energy/heat and waste products.  The addition of energy to a system can add to or support its structure/organization and will always result in a build up of heat that must be exhausted.  If it can’t ‘waste’ this heat into the surrounding environment the structure will degrade, its functions, degrade.  In the case of the sand sculpture, this will happen quickly as the forces that play across the beach level it.  Organisms, with our own particular structures and internal dynamics, have the capacity to counter the forces that would otherwise degrade it.  Because these forces are regular and are exercised over time, organisms require a balanced flow of energy to maintain themselves.  Think of your house or car which requires regular maintenance and service to keep it in a highly functioning state.  What does this have to do with what I’m discussing here?

Living organisms have very low entropy…they are highly structured, very far from a random spread of molecules…they exist far out of equilibrium and are maintained there by unique and necessary energies flowing through them.  Every individual organism functions as a  system, complex, integrated, whole, definable and ‘separate’ from its environment, while, at the same time it is in a direct and dependent relationship with it, upon the ambient conditions it provides, its energy contribution and its capacity as a ‘sink’ to absorb the waste.  Without energy being added, organisms have no chance to exist.  Take away its supports and an organism begins to immediately degrade until it fails catastrophically in death.  We humans have an extremely low probability of existence, yet here we are.  It is much he same story for any organism.  In this universe life would seem to be anomalous existing outside of the Laws of Thermodynamics and the inevitable progression of entropy.  We should be breaking down…or shouldn’t we.  If the universe tends toward high entropy, a randomized state, without energy available for use, how is it that organisms and stars still exist?  Why haven’t they all wound down, utilized all their energy and died?  Winked out or gone super-nova in collapse?  The universe has after all been going on for nearly 14 billion years!  The universe operates at scales incomprehensible to most of us.

Today organisms continue being birthed, species evolving and no doubt others coming to be…while they either adapt or not to changing conditions.  There are believed to be alive today more different species than there have been at any previous time in Earth’s history.  Living organisms have been on a path of continuous differentiation, adaptation and speciation.  At the same time new stars are forming while others wind down.  Everywhere we look individuals are dying, while new ones take their place, even expanding their numbers in innovative ways through speciation, biotic communities becoming more diverse, more complex and inter-related.  Each organism runs through its own particular life cycle, its body degrading as a result of injury and oxidation, a process closely linked to the same process that fuels its growth, development and maintenance of its own systems over its lifetime.  Through continuously acquiring energy, taking in necessary nutrients, an organism staves off its own death, allowing it to balance on the entropic cusp, in a state between the improbable low entropy and the inevitability of high entropy.  Life can only exist in this dynamic state strung tightly, between life and death, in a kind of tension.   Here on Earth the sun powers all of this with its continuous contribution of radiant energy.  Reproduction, adaptation and radiation of species pushes organic life ahead, consuming the energy they have harvested themselves from the sun and from the ‘bodies’ of others they consume, transforming it into their own tissues, excrement, waste heat and our creation of artifacts, the stuff of civilizations, which themselves degrade from the moment of manufacture.  Organisms continuously cycle energy through themselves, transforming matter, in the cycle of living, dying and returning. 

In a universe which ‘should’ be ‘winding’ down, with stars burning out, what is it that pushes life ahead?  Is there a companion ‘generative force’? A natural ‘law’, operating in opposition to this long slide toward high entropy.  In chemistry many patterns appear forming structures from particular reactions that repeat in ever more complex ways in more organisms themselves which are becoming more complex.  These structures do not spring spontaneously in disconnected fashion from a random, amorphous admixture of chemicals…the shapes and patterns they create tend to reappear, integral to the very structure of the molecules, tissues and organs they form, the shells of mollusks, the pattern of striping and spotting in big cats.  They form identifiable patterns, probable, intricately unique, precisely unpredictable, that follow from life and the chemical processes of which they are a part.  ‘Drive’ something appropriately and its physical/chemical characteristics will result in a particular pattern or structure.  These are the products of this flow of energy from low to high entropy, transformed in the process of creating these identifiable patterns and resonances in an organism, the material, through which they pass, while doing so in a conservative manner. 

In the vast space between the stars, where there is little more than the dark matter and energy, of which we know so little, upon which to act, there is thus little from which to create these ‘familiar’ structures…such structures are nonexistent in the vastness of most of the universe, but where matter is locally abundant, on planets, energy moves from form to form, sometimes animating it, always energizing it and, depending on that material, their structures and patterns expressed vary widely, the energy moving through them and on to the next.  Earth with its relative density of matter and complexity of structures, ‘resonates’ as this energy passes through it on its way into the low density, ‘vacuum’ of space a volume of unimaginable proportion and lack of density of recognizable matter, a volume with little ability to attract and retain these energies, which instead more simply pass through it seemingly unchanged.  In space photons pass through incredible stretches of space, largely unaffected, retaining their potential for uncounted lightyears of distance dispersing across its vastness.  It is the miracle of mass, perhaps the Higgs boson’s interactions with many of the elementary particles, that create mass, without effect on passing photons, that enables the dance of life, mass, so created, now able to absorb and utilize the energy of photons. 

There wold appear to be a conservative imperative operating alongside the laws of Thermodynamics. ‘Thou shalt not waste energy when other options are available….’  Despite this winding down into a state of high entropy/low availability, the universe works to use whatever means are available to it to capture and transform itself and thus acts conservatively…not letting it ‘go’ in a single rush.  While entropy increases, this flow of energy tends to transform matter, organizing it, increasing its complexity, incorporating energy in its structure, if even only momentarily, before passing it on.  In doing this it serves to conserve energy.  Is this ‘intentionality’? or is it just in the ‘nature’ of the materials themselves to behave this way?  There would seem to be still undescribed ‘laws’….Thermodynamics pushes the  universe, spending and dissipating energy, increasing entropy, while creating low entropy complex structures in a way somewhat analogous to an object, being forced through water creates a series of vortices, whirlpools, each of these a dissipative structure, in their case winding down without additional energy added, the flow of the water forming these structures around the mass of rocks.  These resultant dynamic structures are a direct result of the flow of energy through and around matter. 

We, all organisms, are not accidents easily erased by time, but part of an incredibly long process that is moving forward.…If this is true, we commonly sell ourselves short, living our lives for the short term, blind to the larger purpose and so act rashly, selfishly in the now, while the rest of the collective system, presses on.  The road to high entropy is not a short one step of consume and be done with it, it moves through stages, conserving, continuously ‘recycling’, rebirthing, reimagining itself.  The universe, effectively, ‘stewards’ itself.  It is not simply ‘burning’ itself up.  We do not know how long this universe will last so why do we race about so, ‘spending’ it and our opportunities so profligately?

Remember CHNOPS? Those carbon, hydrogen, nitrogen, oxygen, phosphorous and sulphur atoms which comprise the vast bulk of every organism?  Along with those more minimally required elements, calcium, iron, magnesium, etc, these comprise the ‘bodies’ of every organism.  Each one of these has its own attributes, capacities and limits.  If they were merely additive, no life would exist…but they aren’t.  In life they become infinitely more complex.  Nor are they a random arrangement of notes in a musical score, they form a recognizable structure, an organism.  They resonate with each other and ‘tune’ their energies in that peculiar way, one that we all know when we see it, when we sense it.  The energies of each individual electron, proton, neutron, each quark, meson, boson and graviton, Higgs particle present, each impossibly small bit of matter, resonating in their own particular way, unique, in each organism, related and descendent from its progenitors, so highly tuned as to become something else, entirely, something more.  It is not the parts that comprise the whole, it is the precise configuration of the whole that defines itself.  A whole of still unimaginable complexity, vitality and fragility.

The existence of each organism works to assure the continuation of itself, but not at the cost of the ‘whole’, perpetuating itself over the course of each individual life.  Each organism is a product of these forces and the larger community.  The broader community of individuals, in a very real sense, is acting collectively adding complexity and structure to the system as energy flows through it, powering organisms, ‘sharing’ a portion of itself on its way to higher entropy.  Each individual, each species, all of the communities play their role and make their contribution to the ‘greater good’ as life trundles along on its own path, unfolding.  We too are a part of this process.  Our consciousness, itself a product of this, can lead us down a path of distractions, which can turn into doubts, then acts of hubris, shortening and redirecting our own path, as we focus our attention away from the larger picture, but our ‘failure’ does not alter the larger purpose or ‘intention’ of the whole…we merely shorten our own role upon the figurative ‘stage’ and shift the outcome to a ‘new’ more probable future.  The process and the flow of energy goes on.

The study of science, quantum mechanics in particular, causes one to question even the most basic everyday assumptions we may have and are blind to.  It is a science that refocuses us, realigns us.  Our world is no longer flat with sun and stars pulled by the gods around us.  Indeed it never was, but so many of us once believed.  Others saw the earth riding the back of an immense tortoise, while others saw the world emerging out of a ‘dream world’.  Many traditions, many creation myths.  It is only under our consideration of the vast range of possible conditions that we may begin to see this…conditions I’ve attempted to explain.  Why does one organic acid form and not another? What accounts for the specific molecular structure of an organism or anything else?  Of all of the potential thousands of proteins, each with its precise and lengthy chain of amino acids in folded structure, why this particular sequence and shape?  Why do so many of these repeat across species lines?  Matter, the elements, provide the fundamental building blocks which comprise every object, every artifact, every organism.  The vast majority of any organism closely follows that of any other at the level of its component parts…because we are ‘related’ born out of a shared process.  The universe is an endlessly intricate network of success stories…and extinctions.

How is such a thing possible?  How can the larger ‘system of the Earth’ generate life?  How can that even be suggested?  When we live immersed in the same system it is hard to gauge its influence on us.  We don’t need to understand oxygen to benefit from it un-sensed in the atmosphere.  Most of us have little understanding of its oxidative effects on the chemical fuels we consume or its role in degrading our own tissues, but live here we do and we are absolutely dependent upon 02’s availability within a limited range of concentration in our atmosphere, neither too much nor too little…just as surely does every other organism…at least the aerobic ones.  Too much 02 leads to ‘oxygen poisoning’, which causes lung damage, creates an array of symptoms including trouble breathing, even death…. 

(The fossil record, and our understanding of animal metabolism, now tells us that during the Paleozoic era, around 300 million years ago, huge dragonflies zipped around with wingspans stretching more than two and a half feet, dwarfing their modern relatives. Back then, the planet’s atmosphere had roughly 50 percent more oxygen than today.  Without circulatory systems these prehistoric dragonflies would not survive today’s lower 02 levels, and in fact they could not, disappearing from the Earth’s inventory of organism’s as oxygen levels dropped.  At today’s concentration the gas would be unable to diffuse fully into their bodies to support their internal metabolic processes.  Such concentrations would prove fatal to us.  These conditions would have also set the stage for extreme flammability, which was, at the time, partially offset by high humidity.  The conditions of this world, though relatively stable, are not fixed either.  As they change so do the species which inhabit it.)

When we find ourselves as individuals outside of our comfort range, we make adjustments so that we can survive the lack of water, the extremes of heat and cold, the lack of food or the other wise inhospitable or life threatening conditions we might encounter.  We plan and we know that too long outside of supportive conditions, we, and many of those organisms upon which we directly depend, will die.  We endure and we compensate.  Other species lack our adaptability, our tools and our access to outside energy sources  Life happens all around us, all of the time, when conditions are right.

What is this ‘life’ thing?  What does it mean to live as an organism?  What is this state that we all seem to share?  I keep returning to this question.  I have seen life defined as a state of energetic disequilibrium, the fine point between stasis and chaos where the reactions within us balance between the sub-critical in which life would fall back into stasis, and the supra-critical where the reactions we are so dependent upon would race ahead and consume us.  It is a dynamic and seemingly precarious balance, reliant upon precise control and a continuous expenditure of energy,  with a proportional ‘wasting’ of excess, to keep us there, ’balanced’ upon a precipice by the limits placed upon these same structures, each organism.  Organisms are now understood as being autocatalytic, self-regulating and self-maintaining, our particular structures, as variable as they may be between species, drive us all forward through time effecting, catalyzing, all of our necessary biochemical reactions, maintaining our metabolic functions in balance as well as the overall health and vitality of our structures themselves, our bodies, our cells. 

We all produce the ‘activators’ our systems require, the catalysts as well as inhibitors to slow these same reactions, the two working together to create a dynamic ‘stasis’, produce the necessary pulses, cyclic waves of production of the staggering number of compounds required through the many stages of even seemingly ‘simple’ functions, transforming what could otherwise be a runaway train of chemical reactions, resulting in the ‘explosive’ death of an individual.  Each organism must be able to perform this dance, unbroken, throughout it’s entire life.  ‘Success’ is found in the efficacy of the organism, both in its capacity to maintain its own health within the reality of its environment, to fulfill its role in the larger biotic community and in its ability to reproduce.  In the end, our fitness as human beings, does not rely solely upon our ‘superior’ brain our opposable thumbs or our ability to wield tools and weapons.  Any organism’s fitness rests on the countless reactions that are ultimately, us. This goes for all of us, bacteria, fungi, plant and animal alike.

Fitness and Survival

Evolutionary scientists refer to ‘fitness’, as the ‘fit’ between a species and its larger environment.  In a very real sense an organism resonates as a whole with its environment…it ‘fits’ in amongst all of the other component parts forming a larger whole.  Each individual is necessarily always in relationship.  It is much more than an individual, the simple sum of its component parts.  When an organism is born or created, it carries within it its animating energy, ‘shared’ from its progenitor…the ‘spark’ of its creation in a real sense, gifted to it.  Integral.  Whole.  For each species, each individual, this ‘balance point’ is slightly different, its metabolism set and ‘governed’ by its species and individuality, at its moment of creation, sometimes ‘burning’ faster’, in other species, slower, linked also to its complexity, it’s environment and its activity level.  

Organisms are not cobbled together with generic operating instructions.  They have to ‘fit’, be ‘tuned’ to resonate with their environment and larger community.  They do this from the very beginning, from the moment of their conception, the joining of sperm and egg, or the division of a one celled organism. Each multi-celled organism follows its own unique development, from zygote, to blastula and on, whether developing inside an egg loosed within its environment or held in a uterus, whether seed or spore, the embryo forms consistent with its inherited patterns, its genetic instructions, in concert with its essential and supportive environment.  At every step the energy flowing through them, animating them, the organism amplifying and modulating it to translate itself perfectly, enabling its transformation and resultant life. The specific proteins, tissues and organs, their particular organization within their structure, are ‘born’ of this dance, never missing a beat.  All of this originated within the context of Earth and the specific environments experienced by each organism within a shared set of parameters.  Every success following from previous successes woven into wholes.  Our bias is clear in everything we do as individual humans.  We tend to see ourselves as individuals, separate from other individual humans, we do the same with all other species, as we pick each one up and examine it, assess its value to us, missing the context as we do our own.  We generally fail to see our embeddedness, distracted by the lie of our own ‘independence’.

The success of Earth’s system of nature is self-evident in every lipid, every protein, every strand of DNA, every organism no matter how simple or complex.  Every organism is, in a sense, a reproducible miracle.  It is very much as if nature is ‘learning’ as it goes along, building ever more complex molecules and organisms as time passes adding to its ‘library’ and repertoire.  It does not ‘forget’ once it makes an advance or a change.  At the same time it doesn’t only ever after repeat the new iteration…it adds it to an increasing repertoire at least until an extinction event wipes a species away, but even then it does not forget how to make deoxyribonucleic acid or insist wrongly that it be ‘built’ with sucrose rather than ribose sugar.  These patterns of molecules, cells and tissues, are not lost though they may be configured in different patterns forming different organisms, they are reconstructed time and again by the precursor chemicals, cells and organisms before them.  Of all of the countless possibilities, the ones that work are most likely to be made again following proven and established patterns, some would call these ‘habits’, evolving.

There is a system at work here and though we cannot define it precisely into inviolable laws, at least at this point, we can describe what seems to be happening mathematically.  We can propose hypotheses and theories that link the miracles together.  Whatever theory we accept, it will never define away the miracle of what continues to happen everyday.  That miracle only goes ‘away’ if we instead adopt an indifference to life, if we blind ourselves to it by demeaning it, forcing it into a world of the mundane and mediocre.  Life will always possess intrinsic value, it is us which is the problem when we fail to recognize this, when we lose our sense of wonder, amazement and reverence for all of the life around us, our links to and dependence upon it.

Wholes vs. Individuals and Parts

This view of evolution requires that we take a step back from our ‘normal’ approach in scientific inquiry in which we have accumulated a great deal of knowledge gained through a reductionist and atomistic approach, in which we’ve broken our subject into its many smaller parts, and reinterpret it in terms of ‘wholes’, of complex, real world, working systems, not just an agglomeration of parts…and it is through looking at this in an essential, natural, wholistic way…not partial sets, each belonging, each having a place, that we we can ultimately make sense of it all.  This approach takes the position that the ‘whole’ will never be ‘understood’ completely from a study of its separate parts.  There is an intrinsic quality of a whole that is missed in any dissection of its subject….In our study of life and organisms, there is a funny thing about ‘wholes’, organisms, they are complete, coherent, integrated, even at their beginning, well before they are capable of ‘independent’ life.  This may sound like an oxymoron, but it’s not. 

Organisms do not transition from zygote to a fully formed adult, or evolve from one species to another in incomplete ‘steps’.  To be ‘incomplete’ in this sense would be to be fatally out of balance, dead, unable to ‘conduct’ the sustaining flow of energy through its system, its structure, disrupted by ‘breaks’.  Death and extinctions are certainly abrupt, while the processes of differentiation, of speciation and radiation, of ontogenesis, of the physical development of the individual, is itself one of shifting from whole to whole smoothly, seamlessly, every moment along the way, alive, even though it may be quite dependent…dependent on the mother within which it is developing, or, ‘simply’ supported by its environment which is, and always will be, essential to its survival. 

This development, this smooth transition from whole to whole, is not a concept foreign to physics.  Quantum physics has taught us that at the subatomic level, matter ‘switches’, makes so called ‘quantum’ leaps, electrons appearing in one position then another, particles switching from one to another.  Chemists have found such action in certain chemical reactions, in the making of molecules.  At another scale matter commonly undergoes phase shifts, as I’ve described elsewhere, absorbing or emitting energies in the process, moving from solid to liquid to gas, or in some cases, to the fourth state of liquid crystals.  Organisms already possess multiple rhythms, long and short term cycles of function, producing one product/outcome, then another before returning to the first…necessarily, necessary, because to not do so will deprive an organism of function and required metabolites…and it will die.  Two necessary states, neither of which alone is enough. 

Unique structures are formed once in the lifetime of complex multi-celled organisms during, and only during, a particular stage of their development.  While a tree continues its cyclic production of leaves and flowers, we with our highly specialized organs do not continue growing additional eye balls or hearts.  We simply produce new cells to replace those worn out or oxidized over time.  Why should evolutionary biology be any different?  If a smooth transition is not possible an individual dies.  If conditions have changed so much that a species cannot adapt to them, it goes extinct.  Organisms carry within their DNA redundant and/or so called ‘junk DNA’, that some suggest provide an elasticity to the process of evolution, that when these genes are ‘reactivated’ they can provide new possibilities, that silenced patterns can be reawakened altering morphology and function, exchanging ‘old’ proven patterns for those that no longer meet the demands of present conditions and that the same resonances that integrated the organism ‘before’ provide some assurance that this ‘new’ organism will be whole and resonate similarly.  A species is not an identical collection of individuals.  An individual is a product of the species.  The species is something apart from its physical manifestation.  It is a set of patterns which are themselves a response to nature and its conditions.  A species is an ‘answer’ posed by nature’s ‘question’ in this particular space and time.

Single celled animals are produced whole and functional without a transitional maturation phase, going from whole to whole…the cell ‘doubles’ before it divides/separates into two individuals.  Certain other species such as insects and amphibians go through one or more metamorphoses or instars, in which a living individual, ‘withdraws’ from the world, and reconfigures its own structure in a continuous process of life.  These changes can be radical as an individual develops entirely different structures, restructuring its morphology.  Others mature over time, developing reproductive organs and capacities at particular ages.  Perennial plants mature similarly over time delaying their reproduction as they prepare themselves, in some cases changing their physical form in the process. 

Every organism that undergoes sexual reproduction, goes through the two stage process called ‘alternate generations’, first forming a gametophyte stage, which produces and releases unsexed spore which upon ‘germination’ form the spermatophyte.  The spermatophyte, upon reaching maturity, produces male sperm or pollen and eggs or ovum.  In all higher plants and animals this transition is largely unobserved as it occurs within the mother plant.  In more primitive plants like ferns, species undergo a distinct gametophyte stage outside of the ‘mother’ with an entirely different morphology as it prepares to then produce male and female gametes which will interact outside of the body to begin the growth of the spermatophyte stage.  In more ‘modern’ organisms the gametophyte stage is protected internally, can be very small, existing for a very short period, especially in comparison to that of plants like Ferns.  At no time in this maturation process does living stop.  Nature has found ways to relatively seamlessly transform the individuals of various species wholly. 

Higher more complex multi-celled mammals, birds, fish, insects and reptiles, develop within the ‘mother’ as tiny embryos the fertilized  egg stage, the maturing spermatophyte stage.  ‘Mothers’ either gestate their young internally or lay their eggs where they will continue to develop within their shells or membranes much as do plants.  Higher plants, their embryos held within their seed, are released more widely and in greater numbers, generally, than are the embryonic material of animals.  Animals that birth free living individuals, retain their young in utero under very supportive and ideal conditions, or in the case of marsupials, within the mother’s protective pouch where their young can stay up to 450 days nursing from her conveniently located nipples.  Over their gestation periods mothers invest their own energy and nutrients directly into much fewer young, compared to the several 100,000 others may produce and release in the form of spore or seed.  This was an inherited process.  Organisms did not ‘decide’ this at some point in the past.  We humans did not choose to concentrate our reproduction to primarily single individuals…we evolved this way, each increase in complexity preparing the way for the next.  We did not develop independently, rather we did so ‘inter’-dependently, fully integrated into the whole web of life.

Most organisms release their eggs/seeds/spore out into an environment in high numbers…in which most will fail to reach maturity.  Conditions vary widely for success from species to species, each ‘tuned’ to a particular niche.  The cold freshwaters of a stream are such for Salmon and Trout, conditions which would be fatal for countless other species.  Whichever the species its earliest embryonic phase is the most fragile, the most precarious.  When we humans choose to ‘husband’ individuals we strive to reduce all threats to them to assure that more live and thrive as we do in farming, ranching, producing nursery stock or ‘growing,’ chemical products for the pharmaceutical industry.  While that seed of an individual plant is capable immediately of ‘independent’ life it too is still supported within the cradle and womb of its environment and its chances of individual success may be vanishingly small.  Most seeds never germinate and develop, many are eaten by other organisms.  Those that do succeed, do so because of the conditions within which they find themselves.  Those conditions aren’t found in space, on Mars or, for most, outside of their natural ranges on Earth.  In this sense, they are rare.  They cannot be taken for granted or squandered.  Supportive conditions are essential whatever the life form, whatever stage it is in.

Human independence is a fiction, possible only with our ongoing denial of relationship.  NASA’s Biosphere project and our limited forays into space underscore just how dependent we are.  It is only when we take notice, stop and take a snap-shot, freezing a moment in time, that there is any ‘fixity’ in an individual or species, just as there isn’t in a river, which is continuously changing in terms of its molecular parts, its eddies and flow, as well as that which it carries along in its flow.  We see the shape or form and mistake it for the ‘thing’ itself.  Wholes, organic, living wholes, organisms, are not assembled out of a stock of parts, they are not interchangeable, plug and play.  They each develop, through the division and differentiation of their own cells, in an accumulative process, supported by their environment, in the broadest sense, both external and internal. 

Some have written of multi-celled organisms as a kind of community of cells combining into various tissues and organs performing specific functions to provide for the whole, while single celled organisms are self-reliant though in some cases, such as slime molds can join together and form a functional whole for reproductive purposes.  Arguably, these are two different strategies to solve the problem presented by one’s conditions.  The goal being the expansion of life and the stabilization of its processes as it moves on in terms of evolution.  For many species an individual literally contains countless other species that perform needed functions within them, internal populations which shift themselves over time as their conditions vary in ways analogous to living communities in the broader environment. These are ‘free’ organisms living in a very select environment, the bodies of other organisms.  Bacteria, viruses, fungi and protozoans.  Upon death our bodies are taken over by yet other organisms, decomposers, which scrupulously consume and transform our former bodies.  All of these processes are dynamic.  

Examine an individual’s time line at any particular moment and this is true.  Any organism can only survive for relatively brief periods outside of these conditions internal and external.  We tend to look at an individual, separate from its community, from its relationships.  We ‘draw’ a line around them as if we have thus captured them in their entirety, but any individual is incomplete in itself…it cannot be separated from its community or the system which sustains it, from which it sprang and back to which it will ultimately return.  If we cannot see beyond our limited idea of what an organism is, we can never truly understand it.  Our atomistic understanding of ourselves and other organisms as individuals is incomplete and misleading.  Our difficulty with the idea of evolution is confounded by this same thinking that an organism, an individual, is complete in and of itself.  It is not.  We are used to examining an individual organism and believing that we understand it and we focus on the body rather than on the processes to which it belongs, which are integral to its existence, to what it is and, because of this, we miss something vital in our understanding of life and evolution, the creative/generative process that produces this, from which we are never separated.

Energy, and its flow, is key to life.  Plants consume energy in the form of sunlight, its photons captured to effectively break the chemical bonds of CO2 and H2O, freeing charged electrons, a high quality of energy, to be used in the formation of carbohydrate, which is then transported throughout the plant, delivered to each cell, where it is oxidized, releasing an electron which will ultimately be used to power necessary cell functions.  The same plant grows within an environment that is maintained within a narrow range of ambient temperatures, in which its functions may be carried out.  In this sense it uses this ambient heat.  Too much or too little and it shuts down.  In animals this energy flow is abbreviated as we cannot photosynthesize carbohydrates directly utilizing sunlight to power the process.  We must consume them from other sources, other organisms.  Either way an outside energy source is required and the requirements for that energy are quite particular.  We consume organisms and through our digestive systems, which plants don’t have, we break their complex molecular parts down into forms which we can transport around our bodies, thus supplying our cells with the basic materials they each need to power, repair and reproduce themselves.  Our digestive systems are ancillary, supportive, of the ‘real’ work that must go on constantly within every living cell of every organism’s ‘body’.

We cannot build a fire, put on a kettle and put an intact plant or animal in it to meet its energy demands, no matter what temperature we heat it to.  We cannot connect positive electrodes to every leaf on a plant, its roots firmly in the ground, to provide the electrical charges that every cell in its tissues require, the plant held in perpetual darkness, with any expectations that it will continue living and grow.  Any organism’s energy requirements are very precise.  Just the right form, delivered at just the right time, precisely when and where it is needed.  Organisms require the flow of ATP (adenosine triphosphate) molecules, in multi-celled organisms, many trillions of them, which they themselves create in their mitochondria, to power their many coordinated internal processes.  ATP functions as an organic battery each molecule of it carrying a single available electron.  It can take many for a single step in a complex process within a single cell.  The production and flow of ATP must be continuous.  The alternative examples I purposed above are heavy, clumsy and inappropriate, how ever we may attempt to meet an organism’s requirements directly, energy in its wrong form cannot support the processes of life.

Sunlight provides the initial energy that powers essentially all life on Earth.  It is of high quality, with low entropy.  It is highly ordered, unlike heat which propels atoms, molecules and other tiny bits of matter into random motion, with little order.  Life requires an outside source of highly ordered, low entropy, energy, which degrades into less useful, more randomized, higher entropy energy, as a cost, after producing order and complexity in the matter it acts upon.

Powering Life – Energy Flow, Dissipative Structures & Entropy

The Laws of Thermodynamics speak to the use and flow of energy within all systems, mechanical, living organic and all others.  No exceptions.  Energy is always conserved, never wasted.  It can be transformed, incorporated into structures or broken down and released, ultimately neither created nor destroyed.  Matter itself is conserved as well, it cannot come from nothing or disappear into nothing.  Energy and matter throughout their many transformations are conserved.  When energy is added to matter, that matter is activated at a microscopic level with effects that may be translated into macroscopic, larger, structures, whether those are the transient ‘cells’ formed in a pot of boiling water, the wood of a tree or the heartbeat of you and me.  When that structure breaks down the energy in it, in its chemical bonds, is released. Throw a stick of wood on a fire and it burns, breaking the molecular bonds of its structure, producing CO, CO2 and heat.  The energy contained in that stick’s structure is released, the molecules that comprise many of its cells, oxidized, consumed, in a moment and gone.  A one time reaction releasing heat as the captured energy moves rapidly to a state of higher entropy, randomness, unavailable as it dissipates into the surrounding space, the environment, but momentarily released with such rapidity that it might ‘burn’ other such susceptible materials nearby.  If this heat was captured and used to power a steam engine, some small portion of that heat energy could be converted into useful mechanical energy and utilized to do work, before being lost to the environment.  Energy, can never be transformed with 100% efficiency.  All of this energy, once held in its structure and chemical bonds, that lost as heat, that utilized to perform work, in total, remains the same in amount as it was before being burned.  Energy is held in structures.  The energy required to create a structure is later released as it breaks down.  As more complex structures, biomass, is added, more energy is contained within the mass of the system, the community or landscape.  Structures formed come at an energy ‘cost’, that of waste heat lost as it passes through restructuring the system.  The opposite is also true as these structures are broken down. Throw a piece of meat on that same fire, a product of growth and the meat, already in a state of breaking down as soon as the organism dies, has its proteins more thoroughly degraded and the meat is rendered more palatable and digestible, more available for our own ‘use’.

Any low entropy system is characterized by a higher degree of organization or structure, it is a more ‘ordered’ arrangement that requires energy to create and maintain, an unlikely probability on its own one might think.…in an unbalanced state of disequilibrium, structured, organized, not random.  A system in equilibrium, without the addition of energy, lacks structure.  It is uniformly ‘random’ throughout.  Structure has pattern.  Patterns can be described microscopically in terms of ordered mass, ordered particles, molecules, with intervening space.  This microstructure leads to a particular range of macrostructures.  In comparison the most dense masses are found in the cores of stars where heat and temperatures force atoms to fuse into new elements increasing their mass and density.  Throughout the universe, in response to the prevailing conditions matter becomes more highly ordered, more structured when appropriately energized.  The more ordered the system, the more ‘space’ it occupies, as physical structure is created by ordering mass within ’empty’ space.  A uniform mass, has uniform density and randomized structure.  Low entropy systems/structures will always tend to degrade toward high entropy, randomness.  Gas and fluid molecules naturally become scattered randomly within a given space in contrast to the intricate and complex structure of a living organism.  For example, any given volume of our atmosphere is extremely unlikely to have its component gases concentrate, order themselves into volumes of pure nitrogen, oxygen and carbon dioxide or leaving other volumes devoid of them.  Their arrangement will always tend to stay random unless energy is expended to separate them and then keep them that way.   To create and maintain organized, structured, low entropy systems, higher quality energy must be supplied while the waste from this process, the energy thus spent, is exhausted outside of the body, outside of the system, so that it does not overheat.  Humans continue living only within a very narrow range of internal temperature, closely bracketing 98.6ºF.  A mere 5 degrees above or below that for any appreciable length of time and we die.  That temperature is extremely rare in endless volume of the universe.  We must rid ourselves of the heat we continuously produce.  Our bodies as built are capable of conserving at the low and high extremes only so long without the use of clothing and outside cooling and heating systems.  

No matter what organic system we are talking about a little Shrew, a Rose or a microbe, entropy is produced as  of the waste, every organism ‘wasting’ it in its unbroken chain of metabolism.  Energy is taken in and utilized during these internal processes to produce what is needed, when and where it is needed.  The work of metabolism takes place at the level of the cell, it is not centralized as is the preparatory process of digestion in multi-celled animals.  Every cell is a metabolic engine utilizing its many organelles.  Digestion precedes metabolic activity breaking down the raw materials the organism consumes into those the cells can utilize.  For plants ‘digestion’ of complex organic molecules occurs in the soil, water and atmosphere around it.  Decomposer organisms break such molecules down into their constituent parts which plants can then take up as nutrients.  In the case of many minerals, organic acids, the products of the many organisms of a biotic community, or from the break down of organic ‘waste’, act on minerals within the soil to make them more available to plants.  In other cases, specific fungi, living in close association with a particular plant, utilize their own abilities to supply specific minerals to plants in exchange for the carbohydrates they require to power their own lives.  These ‘fuels’ release energy as the cells consume them.  It is the same within plants and animals their metabolism occurring in every active cell of its living tissues, driven by the energy provided by the carbohydrates produced through photosynthesis and nutrients collected by the roots from the soil and distributed to the many cells, or through the foods the animals eat,. 

The metabolism, the rate of respiration of any given plant, is much less than that of any animal of similar mass, yet it still produces and must discard heat.  Plants and animals live at different ‘speeds’.  Many animals require additional energy for locomotion in order to find food and water as well as to seek safety and protection from unsupportable conditions.  Plants don’t/can/t do this.  For the vast majority of them, once they germinate, their wandering days are done. Additionally not all of a plant’s tissues are alive at anyone time and so do not metabolize, i.e., the heartwood of living trees.  There are many animals particularly among the arthropods and bivalves that produce hard shells which are not alive and must either be periodically shed or grown out of continuously.  Some classes of animals have the capacity to produce heat internally and actively work to maintain their internal systems in ideal conditions while other animals and plants are entirely reliant on the the ambient temperature of the their environment.  Many, such as reptiles, which are ‘cold-blooded’, have limited metabolic capacity and upon consuming a meal, become more lethargic than usual, as they have to spend more energy digesting their meal.

This is what organisms do, their low entropy structures are created at an energy ‘cost’.  Energy degrades, as it performs the ‘work’ of ordering, structuring growth.  The universe is naturally disposed in this way, utilizing its inherent tendency to generate order, more complex, low entropy structures, creating individuals, which ‘capture’ some portion of it in their structures, taking advantage of this inevitable billions of years long slide toward high entropy, moment by moment.  Energy flows across a gradient, moving from a place of higher intensity to lower, never the other way.  Energy acts in this way in all systems, not just within organisms.  Energy moves across this gradient accomplishing work in the process.  From hot to cool, from positive to negative charge.  From high to low pressure.  Dissipation is key in order to keep the gradient effective.  The more complex and ordered the organism, the further out of equilibrium that it is, the more energy it requires to flow through itself the more it must dissipate.  Like an overheated engine, our own metabolism, if heated beyond its functional limits, loses efficiency, creates fever conditions, and begins breaking down its internal structures, its proteins and enzymes…and the system ‘crashes’.

Cells are subsystems within multi-celled organisms.  Each one exists on that fine edge of existence between sub- and supra-critical states, stasis and conflagration.  All are constantly being replenished, rebuilt, to maintain their precarious existence.  Human blood cells, the most common single cell type in us, will be replaced 300 times if we live for 100 years.  We humans spend 20 years or so growing to physical maturation and then three or four times more added to that, +or-.  Other species exist with widely varying lifespans, each one maturing to reproductive age, before declining.  Each remains capable of reproduction for a limited period of its life before declining.  For some they have but one opportunity.  In the case of some tree species an individual can live for several thousand years and be productive for most of them.  Plants overall depend on a strategy of producing a massive amount of seed or spore repeatedly ‘blanketing’ potential sites, sending more seed widely, all in the hope that some very few will ultimately succeed.  Most animals necessarily take a more conservative approach producing far fewer young or eggs and this makes sense as organisms living at higher trophic levels, put any environment under significantly higher consumptive pressures, something single celled organisms can afford to do.  Animals that bear independent, live, young often perish shortly after, while those whose presence/participation/nurturance is required for the survival of their young, such as mammals and birds, generally survive much longer.  Woody plants, which employee a  perennial strategy that invests in a more ‘permanent’ structure, combine this with a metabolism that tends to be slower than that of animals, the two combining in such a way as to produce longer lifespans.  Tree species, living in naturally formed forest communities arguably provide support for other members in a communal effort.  Ecologists often argue that this is the way of natural communities in general as individuals fulfill their diverse roles.  Such relationships give these members a competitive advantage in terms of their fitness and their evolutionary success.

Plants occupy the base trophic level as primary producer and shapers of the environment.  Along with bacteria and fungi they help form the biological foundation upon which higher animal life depends…which in turn shapes the pattern and richness of the vegetation.  These lower levels are essential to the long term viability of all higher levels.  Consequently they reproduce in higher numbers, through their prodigious production of seed and spore, numbers which assure the needed conditions for those life forms above them, able to ‘fill in’ when various catastrophes, large and small, leave the land bare.  Multi-celled organisms, with their increased size and complexity have evolved over the vast span of Earth’s years.  While all can be considered essential each fulfill varying roles in the larger ecosystem.   We are role-players and though we may appear to be very unique and independent, something geneticists may argue, at a molecular and cellular level, we are not.  Our science, with its atomistic approach, has a tradition of focusing on differences and though individuals may be unique and readily identifiable, what they all share is far more fundamental than that which separates them.  Our relatedness is undeniable.

We are not the ‘same organism’ at death that we were at maturity though our physical size may remain very close.  Our cells do not simply age in place.  The permanent woody tissues of trees and shrubs are an exception, however, those woody tissues are not ‘alive’.  Living cells and tissues are much more fragile and dynamic.  Living cells fatigue and break down at different rates throughout an organism’s life, as we continuously metabolize, we also oxidize and degrade our own structures.  Human blood cells last around 100 days, before needing replacement.  We are literally not the person we were in the past.  

Living, is natural…and stressful.  An organism must be continuously maintaining and repairing itself, to remain functional and alive.  As we age beyond maturity our ability to repair and replenish our cells begins to slow.  Over time apoptosis, programmed cell death, begins to dominate and more and more cells/tissues are unable to repair themselves, a condition that becomes more common as an organism passes beyond maturity into a state of decadence and decline.  Even as this occurs organisms continue to rebuild themselves, though at a slower rate, before we are done.  All of these cells and the tissues they makeup are gradually shed from their bodies the energy they contain going with them.  When we do this living organisms must remain true to the SLT, an imperative of all systems and structures across the universe.   Over mature organisms are unable to keep up with their increasing rate of cell death…they run an energy deficit and so decline.  My own 93 year old mother died of multiple organ failure, her system unable to fulfill its needs for maintenance and repair.  If an organism were viewed as a juggler, then at this stage they are simply unable to keep their energy ‘balls’ in the air consistently.  The whole system begins to drag down. 

The waste of discarded cells and energy is passed on to others in the immediate community moving from body to body, level to level, degrading after being consumed, its nutrients and the energies they contain  consumed by others which can take advantage thereby utilizing the energy contained within the remaining chemical bonds, ‘reformulating’ that into new molecules, cells and tissues, what these organisms need at the moment.  Generally, no one organisms breaks everything down into its smallest constituent parts when it consume tissue or another organism.  It utilizes the energy from the bonds contained within the material that it can and, like any organism, restructures it through its own metabolic processes into what it needs, again at an energy cost, the inevitable waste heat that is a product of any energy transformation.  What it can’t use passes through it. An interesting example is hummingbirds  and nectar feeding bats which both possess the enzyme sucrase in their digestive tracts, so do we, which allows them to hydrolize/digest sucrose sugars, something passarine birds cannot do.  Passarine birds can do this only with fructose and glucose sugars.  This makes these two hovering nectar feeders more ideally suited for feeding on the nectar of plants high sucrose.  All will in turn, be passed on. 

‘Food’ is food and regardless of its source, is broken down into useable constituent parts and then transported to where it is needed, along with oxygen, unless these are anaerobic organisms and so do not use oxygen to oxidize in their metabolic processes, later, utilizing these to restructure and reorder them, using information integral to each and every cell which receives it.  At every trophic level organisms utilize this same basic process.  Waste is truly never ‘waste’ as we tend to view, but is instead a resource for the growth of others.  It is the work of much of the single celled world, plants, animals, bacteria and fungi to ‘ring’ the last bit of value out of ‘waste’ and in so doing set the stage for the cycle to begin anew with plant growth feeding off the fortified soil.   What is discarded in natural systems always creates an opportunity for other species, other individuals.  Nature does not waste in the way that we often do.  There is no ‘away’ into which to throw waste.  Nature is the consummate recycler.  Waste energy is ultimately dissipated into the vastness of space.  In healthy natural systems ‘waste’ is simply that cast off from one trophic level to serve as the ‘feedstock’ for the next.  It is an extremely conservative process, effectively following the ‘rules’ of thermodynamics.

I should note here that structures and tissues within different species are not all replaced in the same manner.  The cells of our bones and blood have very different ‘lifespans’.  Plants are also quite different than animals in this respect as well, many of which are directly related to their photosynthetic capacities, their fixity to place and their dependent and direct relationship with the soil.  One example is the core, ‘heartwood’ of trees.  These cells, once produced and structurally hardened over time become set.  They no longer require nutrients, their metabolisms in these tissues are shutdown.  Their purpose is to provide a fixed, stable structure upon which the individual’s living, growing cells, may continue.  Heartwood thus has no active defense systems to stave off rot after injury.  For dicotyledonous plants, like woody trees and shrubs, the living tissues exist in a relatively thin layer sheathing the largely inert supporting structure.  Rot of heartwood is then forever.  These tissues are never replaced and thus cavities can be formed.  It is the living, dynamic cells of an organism which participate directly in their life.  Other tissues of plants also tend to have limited individual ‘lifespans’ while the larger individual continues on, depending upon the species, for hundreds, if not several thousand years, while leaves, bark, root hairs and larger structures are regularly ‘shed’, often replaced on a seasonal schedule, the waste going back into the soil feeding other organisms in a very large supporting ‘cast’.

Energy ‘moves’, from organism to organism, structure to structure, transformed in the process, ‘holding’ it in these dynamic structures, for a moment, in a never ending process, the energy, enabling both the creation of the structure and permitting its ongoing existence, combining in the moment, none of this ‘reversible’, instead recycled.  The point here is that matter and energy are always ‘conserved’, they are never lost.  Energy effecting and held in structure, mass, then, when its structure breaks down, releasing that energy.

Under controlled conditions in a closed and limited lab chemistry experiment, many reactions are reversible, the products of their combination can be broken down into their previous existing parts and repeated back and forth.  This can also be true in many industrial chemical processes, but this isn’t true within ‘open’  complex dissipative structures, some of which we recognize as organisms.  While there are commonly ‘pulsing’ cycles which occurs within organisms due to the nature of many of their reactions, the larger structures are not reversible and the individual matures and ages.   An organism cannot move from advanced maturity or decadence, back into its younger more vital self.  Many physicists argue that this irreversibility is the reason for ‘time’ as energy, moving toward higher entropy, plays out in a series of non-reversible events creating unique structures that are here and later gone, perhaps replaced by their progeny or not.  The flow creates the ‘time’ in which life occurs.  Life itself exists in a string of moments and cannot be removed from them.  Life is both enabled by and dependent upon this process. the same process that results in an organism’s decline and death.

Powering Cell Growth: the Role of ATP

So, how do organisms grow?  By what ‘magics’ do they exist at all?  If organisms are highly organized complex structures how do they arise out of less organized simpler structures?  Where does the energy come from that drives this process?  If it requires the timely and specific forms of energy to do this, what organizes and limits this?  The Laws of Thermodynamics still hold…always hold.  What happens when we eat?  What happens when a plant utilizes the energy it captures and holds within the sugars it has created?  It uses that energy to ‘build’, it organizes, it restructures and maintains itself, lowering entropy, in a continuous process, ‘building’ that energy into itself, informing itself, while at the same time, its internal structures are breaking down, continuously, and excreting waste from its consumed ‘fuel’ and shedding cells too aged or damaged to continue.  Life exists on this energetic treadmill.  Once you step off you rapidly decline into death.  Physicists sometimes argue that mass, the stuff of  matter that comprises the physical bodies of everything we ‘experience’, is itself structured, organized, informed, energy.  Energy acts on itself, ‘building’ and life happens at that ‘burning’ edge of creation and dissipation, in that moment.

Almost every organism utilizes the same process of glycolysis, breaking down the glucose sugars it has produced or consumed, ‘harvesting’ their electrical charges.  Biological systems are themselves complex and redundant.  While certain processes, such as the formation of Adenine Triphosphate, ATP is synthesized primarily within a cell’s mitochondria, it is also a minor product of glycolysis.  Other molecules are formed from it as well, molecules that help set the ‘stage’, create the conditions for the mitochondria to perform its major function, the massive production of ATP.  Within each cell mitochondria number into the thousands.  Within each one are the complex protein macromolecules called ATP synthase, which are essentially little ‘organic machines’ driven by a proton gradient, high concentration on one side of a membrane, moving through it in a very structured manner, powering the ATP synthase, on the other ‘side’, reconstituting ATP from the spent Adenine Diphosphate, ADP molecules, the ATP synthase reattaching a single phosphate to the depleted ADP molecule.  These contain high energy bonds which are utilized throughout the organism.  Energy is thus stored in the highly mobile ATP molecules, which serve as batteries to power the cell. 

As organisms pass into decadence, when they become over mature, an organism’s systems begin to lose the capacity to ‘repair’ themselves, their capacity to reproduce reduced and, losing their capacity to self-regulate, to limit the production of certain other cells, such as with cancers, pushing themselves inevitably further out of balance until such a time that the system and organism fails catastrophically, no longer able to maintain its integrity as an organism, in its state of dynamic, dissipative, disequilibrium….

These structures, organisms, animated by this flow of energy, are attuned to their own particular flow in a manner similar to the tuning fork, the flow effects the ‘performance’ of the structure…they ‘resonate’, ‘exciting’ that structure when they are in harmony.  The harmonics involved are not those of sound.  They are a response to the structure and complexity of the organism, an expression of its finely ‘tuned’ and complex self.  As I wrote before an orchestra, its conductor, its music and the physics of all of the conditions within which it finds itself driven by the energy flowing through it producing beauty and structure, readily recognizable, but never exactly the same twice.  Any organism is a much more complex structure than is that of a carefully constructed tuning fork, its ‘response’ to this flow of energy much more complex and attuned….Unlike an orchestra, when an organism is driven by the appropriate throughput of energy, it expresses itself, all of its systems and processes exist in a balanced relationship, self-reinforcing, self regulating, performing internal maintenance in an expression of what it is, a logistical and functional masterpiece, performed at a level of the highest fidelity.  While vital and healthy this structure and flow leads to, even ‘directs’ the physical and temporal structures and functions which is each individual and community of individuals with which it is in relationship.  We and our nearly countless organic companions are not machines in the mechanical sense we might believe, but ongoing expressions of nature and its ways.

When a multi celled organism begins, when that tiny sperm fertilizes an egg, the process of development and growth begins.  At one time our concept of ontogenesis, the development of a fully formed individual from that zygote to its embryonic form, was one of an embryo, a fully formed individual, but tiny, which simply grew in size over time, all of its organs and structures manifested.  We’ve known this not to be true for a very long time now.  The zygote is a diploid single cell, a cell that contains a pair of chromosomes, one each contributed by its parent, but still a single tiny cell.  For any organism, plant or animal, this changes very predictably through a series of cell divisions and processes of complex differentiation, each such division, precise, ‘tuned’, setting the stage for the next.  In the zygote stage, the differences between species is not readily observable, tissues, organs and larger physical structures, are unformed and nonfunctional, a Juniper tree would look very much like an Orangutan.  After each division of cells differences gradually appear in the developing embryo and continue after birth in animals and, after germination, in plants.   ‘New’ structures form. 

In seed plants, the tiny embryo develops within the seed before germination.  At every moment during this process the developing individual is supported by its environment and the flow of energy through its structures, its genetic information selected and expressed only and when needed, precisely, to assure healthy development.  Each gene is expressed or suppressed at any given moment in the process. Tissues form into structures and organs on ‘schedule’, the individual, continuously animated by the flow of energy through it, resonant, attuned, nearly identical to that of the parent(s).  Development is highly coordinated and sequential.  This is why particular nutritional deficiencies may be problematic at one stage of development, but not during others.  Though ‘incomplete’ organisms are, nevertheless alive throughout the process, they are incapable of independent living.  We are not inert and then at some stage sparked into life.  We are alive at every stage, whole, as our complexity and ability to function ‘independently’ increases.  Mutations, aberrations, are ‘tolerated’ only so far, beyond such a point at which the pattern, its structure become non-sustainable.  At every stage of development the flow of energy sustains the individual and this flow of energy itself pushes these dynamic structures into an efficient and efficacious system which strongly resembles the parent(s).  Ontogenesis, the development of the embryo and immature individual, are dependent on the ‘mother’ for its nutrition and support.  This system is not at all random or haphazard, it is in fact the opposite, this internal flow of energy acts to help determine, create and sustain organic structures.

This same kind of sharing, of conserving energy, occurs at all levels within the Earth’s complex web of life.  The larger ‘community’ within which an organism lives, is just as thrifty with and dependent upon its use of energy, if not more so, as the shed organs, tissues and cells are utilized by countless others.  Life is never ‘one and done’.  All are necessarily linked to others.  This process occurs across the many trophic levels as individuals consume one another.  It occurs when an individual dies and its component ‘parts’ becomes ‘available’ to a wide range of decomposers.  It happens, perhaps even more importantly, to us all while alive, whether hale and hardy or sickly and under attack, by disease and parasites.  We are each hosts to our own communities, ‘composites’ of individuals each playing their role, many essential to our own health, in the long winding down of the entropic dance.

The flow of energy works in creative ways, even generative, through this harvesting and cycling. Energy informing, transforming matter, moving it into highly structured, dissipative, patterns toward more complexly organized forms while discarding or excreting ‘waste’, which exists at higher entropic levels.  Never-the-less these discarded and decaying structures contain energy within their remaining structure which cam then be utilized by other organisms.  There is a conservative ‘tenacity’ within this system as it ‘clings’ to its available energy on Earth or anywhere else, each environment with unique conditions and limitations, at a particular stage.  The universe does this naturally, purposefully, utilizing what it can at each successive step within the limits of a system’s immediate conditions.  One needs to keep in mind that the flow of energy creates opportunities as it restructures matter. 

When an opportunity arises, when a particular niche becomes available either because of a change in conditions, be that a result of a change in ambient conditions, temperature, humidity, the availability of an atmospheric gas, the extinction of a species or its extirpation from a particular region, landforms changed by volcanism, the uplift of mountain ranges or the more gradual changes wrought by erosion or the even longer scale changes of shifting continents over geological time scales, new species may arise, built from older patterns, the flow of energies, having shifted slightly or grossly, life itself becoming even more so the ‘yardstick’ by which organisms are judged for fitness.  The larger the niche, the larger the opportunity, the ‘bolder’, the more creative the ‘response’ will be to fill it, to extend this process of increasing complexity, the more intricate and entwined the relationships between the ‘participants’.  It is a billions of years old pattern.

Within an open non-equilibrium system the flow of energy produces a gradient, a difference, energy moving from lower to higher entropy driving an organism’s, the system’s, processes, following its own as well as the strictures of the larger system it is ‘nested’ within.  The same process is underway in any open system on Jupiter, in any organism, in fact in any other ‘space’ to be found in the universe, but, again, each of those responses will be unique to a specific system given its conditions and ‘materials’.  This isn’t my idea.  Scientists, mathematicians, around the world, are studying the capacity of natural systems to ‘self organize’ to increase in complexity and balance these ideas out with what might at first seem to be in direct conflict with the SLT.  Natural laws, unlike human laws, cannot be violated.  We are beginning to find that as conditions change and evolve the very laws that direct this process may evolve with them.  The universe may not be as static as many claim.  There is more to be learned.  Life follows natural physical laws within the limits of the universe.  It is up to us to discover and define them.

The Earth has been in this generative/conservative process, creating complexity from its beginning…and will continue to be so as long as the Sun continues to power it.  The complexity of the Earth system leads directly to what is here now and what will follow in the future, a ‘nested’ system of increasingly complex, dissipative structures.  Human society’s highly consumptive, profligate use of energy today, our destruction of intact landscapes and their living communities, is ‘undoing’ much of this complexity daily, undermining the very conditions necessary for the biologically rich world we benefit from, ‘freeing’ sequestered energy in a rush of consumption, compromising many other ‘nested’ systems within it now unable to capture and utilize the massive increase of degrading energy.  We are severely compromising the 2 step process Greene describes as we harvest fossil fuels from the Carboniferous period, laid down 299 million to 360 million years ago, for short term gain, beginning with James Watt’s development of the steam engine which could burn coal in 1769, escalating exponentially through the 20th century.  We’ve thus consumed much of this in a mere 250 years over burdening the environment with waste heat and carbon, an environment now with compromised capacity to reincorporate its increase.  Our system is now in the process of adapting to these very rapidly changing conditions.  This would be akin to forcing our own bodies to burn massive amounts of energy while our surrounding environment warms making it more difficult to maintain our own ideal body temperature for healthy life…We don’t do this of course.  When we consume too much energy we store it as fat for the future compromising our own structures, encumbering them.  Even if we could draw off our excess atmospheric CO, CO2,, the Earth’s internal systems would still be compromised, it’s complex communities out of balance and so limited in their ability to fulfill their own life sustaining roles.  We are all linked and bound by the same laws of nature.  Today’s climates are warming and driving a migration of people out of regions that are already too warm and dry.  The once sequestered carbon and the energy held in its structures freed and the carbon tilting the chemical admixture, the balance and constituent parts of the environment, forever shifted from pre-1769.

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