Life Inside the Cell – Waking Up to the Miracle, part 1a

[This is the first in an extended series of three posts, this one on life within the cell, the second, on the evolution of plants, and the third on the New Phylogeny and Eudicots.  Some time ago I began this ‘theme’ with an extensive post on Monocots. This first ‘installment’, concerning life within the cell, is divided into two parts, the first, with the ‘a’ in its title, covers the growth and function of the cell itself and, importantly, the role of water within it.  The second, with the ‘b’ in its title,, will examine the concept of quantum biology and its explanative necessity for life beyond the ‘simple’ construct of cells, tissues and organisms. While trying to understand the ongoing reorganization and classification of plants, I found it necessary to better understand these other topics, what it is that we are ‘messing’ with! ]


I begin here with the cell, what I’ve learned about what makes the cell, its existence and life within it, so amazing, something which should give us all pause, when we consider our own lives and what we do.  When scientists ‘split hairs’ in their arguments on which group to assign a species, when they attempt to link them to their ancestors, so many of which are now long extinct, to understand their relationships with other organisms, they have a purpose.  They are often looking much deeper into what a plant is, what constitutes life and how it evolved.  Phylogeny, the science that attempts to establish relationships between different organisms, different species, to link one to the other across time, is about both the history and the continuing journey of life on this planet.  It promises to tell us much about our own place as well as that of the hundred’s of thousands of other species with which we share it.  Ultimately, if we choose to understand this, it will change the way we garden and our relationship with the many landscapes that cover the Earth.  Our gardens are our own personal expressions, works of ‘art’, and must live within the parameters life has set for them on our little pieces of ground.  They reflect our understanding of the limits and possibilities at work here.  The better that we understand this the ‘better’ our gardens will be, the more in synch they will be with life.  

As human beings we tend to think of ourselves as individual beings, whole and entire, not as composite organisms made up of various tissues and organs.  We see other organisms, plant and animal, much the same way, sometimes even organisms like Algae, which are single celled, individuals, we lump together into the large masses we often see them form into where they live in water, despite their capacity for independent life on their own.  This is a bias of our scale and our sense of ourselves as an organism.  Our bias contributes to our seeing other organisms in the same way, as whole and entire entities.  We do not ‘see’ cells.  We experience our bodies and nature at our scale and when we do look through a microscope or at images produced via one, it strikes us as somehow foreign.  We do not sense our own bodies in their various parts.  While we may feel hungry we do not generally link that feeling to a call from our billions of individual cells for energy.  We don’t understand that our bodies have evolved in such a way that this cellular demand for energy and nutrients is translated somehow into ‘our’ hunger.  I like the use of this particular pronoun, ‘our’, as it recognizes the collection of our many parts into coherent organisms.  In this sense ‘we’ are plural, we are communities living in very close association.  The same can be said for any multi-celled organism, including plants, each is comprised of countless cells, often with very specialized structures and functions.  It is only the simplest organisms that are composed uniformly of like cells.  Whether simple single celled organisms, or incredibly complex and large multi-cellular organisms, each is ‘alive’ and functions internally as a coherent, coordinated, individual, that a single celled organism does this, accomplishing all of its necessary life functions, while a multi-celled organism ‘requires’ its diverse structures to accomplish its ‘needs’.  What do these two, and the wide range between, share in common that makes them alive?

Life Inside the Cell: On Being Alive

Life on Earth today is nothing without the essential processes of photosynthesis and the metabolic ‘pathways’ that have evolved within organisms that enable, support and define it.  Plants today are the only organisms that possess this capacity…and all of this is dependent upon the cell and the chloroplasts that many plant cells contain.  The cell, its apparent simplicity of structure, is in reality a  complex and incredibly well coordinated organic structure, animated, yes, even within plants that remain firmly rooted to the ground, and are defined by their internal processes.  Cells do this with an amazing degree of internal control, capable of all their necessary processes, while at the same time each individual functions in concert with other organisms, responsive to their environment, each contributing as it can including, ultimately, the sacrifice of itself.  Cells are anything but random blobs of undifferentiated protoplasm.  The cell is the most critical development in the long evolution of life.  It is basic to all organisms, including the largest multicellular ones, from the Paramecium to the Blue Whale, the Giant Sequoia to sprawling clonal colonies of Quaking Aspen to the fungi that spread throughout every acre of Earth’s landscapes.  Respiration, the Oxygen consuming activity of the cell, its capacity to form proteins and the enzymes and catalysts that trigger, signal and help coordinate an organism’s many functions, its DNA, with its ‘plan’ and ‘instructions’, the code within every organism…all of these are essential ‘pieces’ of the cell.  The cell has been evolving for billions of years and is continuing to do so, even the single celled organisms like bacteria continue to evolve making micro-adjustments to their changing environment performing their role in keeping it all in balance.   From primitive bacteria came the first multi-celled organisms.


This schematic of a ‘modern’ eukaryotic plant cell is generalized. It is a teaching tool. This is not what all plant cells look like up close. Whether plant or animal an organism’s cells can have very different structures, such as those within the xylem tissue, a leaf or a flowers ovary…they are not identical ‘blocks’ merely put together in different patterns. It does show many of the essential organelles within the cells of plants. The ribosomes, shown here as tiny dots, of which there can be upwards of 10 million living freely within a single cell or attached to the membrane within both the smooth and rough endoplasmic reticulum, altogether which are responsible for the production of a cell’s proteins, varying from the organelle that produced it; the chloroplasts which serve as the sites for photosynthesis…in those cells that ‘require’ them, which transform into other bodies, serving other functions when not ‘needed’; the mitochondrion, singular, each cell will have several, which serve as energy production centers transforming the energy contained within the synthesized carbohydrates into ATP to directly power a cell’s functioning; lysosomes which break down damaged or degraded proteins for reuse; the various vesicles and vacuoles which store compounds, hormones and enzymes for later use and much more. While all cells contain many of these, the cells of more specialized tissues, such as the vascular/structural tissue of a plant’s stem have very unique shapes and utilize the thickened and strengthened cell walls in fulfilling their functions. All of this is coordinated within the organism.

The cells of these more complex organisms evolved to live in even closer association with one another, often taking on highly specialized functions and roles and they did this at the loss of particular functions that an independent cell requires.  Living as part of a larger organism requires that they are able to coordinate amongst themselves the increasingly complex shared functions of the large multi-celled organism, a need well beyond the capacity of the single celled organism. 

Early on in the history of life some single celled organisms developed the capacity to live in structured masses like algal mats floating in water in a way that benefits themselves and other organisms.  Other species tended to cluster around one another for benefits while avoiding other species that posed a more active ‘threat’ to them.  This tendency to live in association is one of the definers of life and always has.  What succeeded tends to be repeated.

On the negative side life has also always required predators, disease and infestation, as a balancing force to help limit the unregulated increases in population that would take place without its corrections.  The world is dynamic and death is essential.  Each organism, in a sense, an experiment, is allotted a limited amount of time to perform and play out its role within the larger process. 

Originally, in theory, early single celled organisms would have an unlimited, indeterminate, life span and would not ‘die’ on their own without outside ‘stress’.  Depending on conditions and species, they would periodically grow, increasing their mass and divide their chromosomes as they ‘split’ themselves in two, forming another genetically identical individual, and then carry on…unless of course they were consumed by another organism.  This type of division, mitosis, continues within the cells of higher multi-celled organisms as they grow tissues and replace old or damaged cells.  These other specialized cells, that comprise a multi-celled organism, have no need for sexual reproduction as they are a part of a larger organism capable of reproducing as a whole.  These organisms grow and replace their specialized cells until eventually this capacity is ‘shut off’ and the organism wears down, degrading until it dies.  Apoptosis.  Programmed cell death.  Their individual cells then senesce.  Whether consumed by another organism, perishing to disease, an overly stressful environment or through this phenomenon of apoptosis, each multi-celled organism comes to an end and with it all of the individual cells that comprise it.  For them the cycle begins anew through their offspring produced through sexual reproduction. 

It is only the gametes, their sexual cells, that undergo the process of meiosis and prepare the way for the sexual reproduction of multi-celled organisms.  These are the cells which have been restructured to contain only one set of chromosomes, they are ‘haploid’, while all other cells of an organism will be double that, or diploid, so that when recombined during sexual reproduction these joined gametes are once again diploid and complete.  [There are exceptions to this, some organisms having more than two sets of chromosomes, a state known as ‘polyploidy’ which effects an organisms ability to reproduce sexually and can effect the size and structure of the organism itself, but that is a topic for later.  Polyploidy is believed to be extremely rare in animals, but would seem to be much more common in plants.]  This aside, the life requirements of any cell are remarkably similar though their ‘relationships’ with other cells varies widely. 

We could speculate all day why this may be, why organisms die, but if one studies the evolution of life, one will eventually be forced to admit that over its 3+ billion years, life has changed on the planet, evolved in its complexity…in step with the changing conditions on Earth.  This doesn’t mean that simpler, more primitive organisms, no longer have a role, quite the contrary, as many of these have proven their absolute necessity for the continuation of life over many millions, even billions of years.  This kind of change is not possible without death.  Whether we understand it or not there seems to be an underlying ‘intent’ that may itself be evolving as the process itself ‘evaluates’ each individual, generation, species and the relationships they are involved in.  

Higher, more complex organisms remain dependent on simpler organisms and their healthy relationships and not just as a food source.  Any organism’s numbers will have limits within any landscape, that will require its death if the system is to remain in balance, also, organisms all have an essential role to play, while having programmed limits to help maintain a healthy balance.  Biological success of an individual does not free it of its role and obligations, not even for humans.  Our notion of ‘the survival of the fittest’ in which the ‘fittest’ comes to dominate all others, as an essential element of the process of evolution is inaccurate, more of a product of our naive and narcissistic belief of our own self-importance.  Today we often justify our aggressive pursuit of our own ends by our ‘short term’ success in attaining them.  This self-serving conception of success is often decidedly counter to the ways of nature as we continue our domination of it in our pursuit for financial gain and personal status and comfort.  This is counter to the several billion years long record of the evolution of life.  Our practice is pushing the entire ‘system’ ever further out of balance by consuming other species and resources in a way that threatens their viability.  As we do this we find ourselves in the position of having support and provide the ‘services’ that a one time healthy functioning system did freely for us.  An ever increasing rate of the consumption or sacrifice of other, ultimately compromises all.  Biological collapse is the more likely outcome of such action.  We have much to learn from our fellow organisms and their intertwined relationships.


Most people define plants by their capacity for photosynthesis.  It startles them to hear that not all plants have this capacity that some have need for neither chlorophyll nor leaves, that some plants are completely dependent upon their intimate connection to photosynthetic plants, but plants they are, as they have flowers, produce seeds and share a genetic line with other plans.  They can strike one as more likely to be grouped with Fungi except that Fungi come from an entirely different genetic line, never possess chlorophyll or flowers.  But photosynthesis is a central feature of the vast majority of plants.  It is through photosynthesis, the splitting of the water molecule in the process of harvesting energy captured from the sun, something we are told about as children, though it is a considerably more complex process than the simple ‘magics’ that were used to describe it to us then, that has proven to be key to both aerobic life on this planet and the ‘success’ of plants as a whole upon it. 

When cyanobacteria first began photosynthesizing 3.5 billion years ago they didn’t produce Oxygen, the world was anaerobic, a world where Oxygen initially existed as a relatively minor toxin and they produced the molecule ATP which are essentially tiny chemical batteries that cells can use to power their metabolic processes.  The success of this process can be seen in the fact that virtually every organism has adopted it internally.  It took another 1/2 billion years before the process within Cyanobacteria changed to produce Oxygen as a toxic waste product.  The world was anaerobic and unsupportive of modern life.  The earliest organisms were anaerobic bacteria and archaeas capable of consuming and utilizing the energies held in the chemical bonds of molecules that would be toxic for more modern organisms.  Cells consume other materials, breaking them down to harvest the energy they contain then synthesizing what ever compounds they might need to live.  This has always been the way.  Different species have different capacities and requirements.  Over the course of billions of years life in all its forms has evolved here while modifying the very conditions under which they live.

It took another billion years for the atmosphere to become oxygenated enough to support aerobic life at which time the more complex Eukaryotic cell emerged. 

These Eukaryotes are more complex than their predecessors, the Prokaryotes, and notedly include a nucleus which is contained within its own membrane.  The nucleus is the holder of an organism’s DNA which is central to sexual reproduction.  Over time these began adding other organelles, along with their functions that were also bound within their own membranes.  These include the mitochondria, ribosomes and various ‘plastids’, I mentioned above.

The process of photosynthesis is, on its surface, a simple and elegant process unique to plants.  While plants, like animals, require energy to metabolize and grow, plants can harvest and transform the sun’s energy building it into the basic compounds which they require to live, including energy rich carbohydrates and the little energy packets that they convert it into, ATP.  Animal life, unable to photosynthesize, or harvest other energy forms directly to convert, store and later use to power their own metabolic processes, rely on the energy contained in the foods we eat, and the compounds contained within its nutrients, carbohydrates, fats, proteins and amino acids, vitamins and minerals, created by or accumulated within the cells of plants, though animals too contain mitochondria which can convert the energy within the molecules it consumes to the same highly available Phosphate rich ATP. 

Plants are ‘autotrophs’, they do not feed on other organisms, but synthesize what they need from their surroundings (Some are, however, either parasitic or hemi-parasitic, drawing all or some part of their nutrition directly from other plants). Animals are heterotrophs and must consume other organisms to live, to ‘power’ their bodies and provide the basic building blocks ‘we’ use to grow and maintain ourselves.  Animals are dependent on plants directly for their nutrients and/or secondarily by consuming other animals that consume plants.  Animals are capable of metabolizing many enzymes, catalysts and compounds that they require, but they still must consume the proteins and many rudimentary building blocks which these are built of, from other sources, plant and animal.  While not commonly acknowledged, animals are capable of absorbing, utilizing, some energy directly from their environment to help maintain their critical systems, both light and heat energy.  The oceans and atmosphere provide these ambient temperatures that life requires.  Were they to drop significantly, all of the biochemical processes within an organism’s body would slow and eventually cease.  Animals and plants both require a relatively narrow range of ambient temperatures within which they can maintain their internal temperatures for their basic metabolic systems to function.  The consequence of moving too far out of this range for very long results in either heat stroke or hypothermia, followed by death if they are to continue.  The same is true for plants.  Despite what science fiction writers might put into their stories, life as we know it would be impossible on an ice planet just as it would be on a planet with too high of an average temperature which evaporated all the available water into the atmosphere, including that from within once living organisms.


The modern, eukaryotic cell, in its most basic form consist of a membrane that contains and shields its DNA and protoplasm within.  The water contained within a cell is essential for its life.  Its membrane and the many proteins which comprise its cytoskeleton help contain and conserve it as the cell performs its internal functions.  Initially these were very simple reflecting their structures.  Over time more complex cells evolved with more complex functions, allowing them to occupy increasingly diverse environments. 

Organisms are very much more than a collection of parts.  As a western civilization we have a tendency to think in mechanistic terms even when considering life, as if it were only a different type of machine, reproducible on an assembly line, energized and maintained like any other mechanism we might build.  But that is us projecting our ideas upon the world.  Life, in a sense, has developed its own recipe, with its precise content and proportions, energized by the very process of its creation, to stimulate particular internal chemical reactions that in this case spark a self organizing and ongoing process, resulting in ‘organisms’ with particular and shared architectures at every scale, organelles, cells, tissues and an overall organizing structure, proven over time, recorded in one’s genetics, complete with ‘operating instructions’ to metabolize, respire and reproduce.  This ‘spark’ seems to be passed from organisms to their offspring through their fertilized seeds or eggs in a continuous line.  The seed and egg are unique in this process, held in a state of a kind of dynamic tension, balanced on edge, teetering, with the possibility of death surrounding it in every ‘direction’.  Ready.  In animals the fertilized egg begins the process within itself almost immediately protected within its membrane or a shell, many animals, developing, gestating, within their mother’s protective and nutritive uterus.  This ‘transfer’ occurs in an unbroken chain.  The metabolism and respiration of living organisms, in turn, contribute to the same conditions an organism requires for life, helps them maintain themselves in an energized state of ‘disequilibrium’ without which an organism dies…and they have a likewise effect upon the environment in which they live.

An Organism as a Living Entity

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

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


Organisms do not burn their fuel in this manner.  They instead ‘digest’ their fuel.  Carbohydrate is delivered to the cell, animals utilizing their larger digestive systems to convert the nutrients into a form the organism’s cells can utilize.  Metabolism takes place in each cell utilizing various enzymes which act as ‘keys’ to unlock molecular bonds freeing the electrical charges that once held them together.  Animals tend to have a higher rate of throughput, especially homeothermic, warm blooded animals, which can regulate their metabolism rates to produce heat that allows such animals to maintain their body temperatures within a narrow ideal range.  Cold blooded animals and plants have overall much slower metabolisms as they have no need nor capacity to ‘heat’ their bodies.  There are of course exceptions to this, some quite interesting, such as in the flowers of the giant Amazon Water Lily, Victoria amazonica, which during flowering can heat their nectararies above ambient temperature to better volatilize it and attract the beetles which alone pollinate it.  Plants then live at a lower ‘speed’ than do animals.

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

All of this involves a complex system of regulation within the cell, the tissue and the organism as a whole.  To do this the cell and the organism must produce the various hormones and enzymes that regulate its various systems, the enzymes that work as catalysts to regulate the necessary metabolic processes.  It must have these ‘keys’ necessary to turn its internal process on and off as needed as well as set the speed of these processes.  Animals of course, at least those capable of physical movement, will also require those to be coordinated in an effective way.  This is one of the central issues for any organism, for it is one thing to have the capacity to do something, it is entirely another to orchestrate it within an organism that is responsive to its environment and the organisms it finds itself amongst.  From cell to cell, between organisms, they must possess the capacity to ‘signal’ the other and then to respond as needed in a timely manner.  Life at every level exists in ‘communities’, living in relationship with other organisms of the same and diverse species in ways similar to the way they must internally so that they are not simply an aggregation of cells, but are functioning and coordinated organisms.  This coordination in multi-celled organisms is more immediate and central to one’s existence, as an organism cannot last long if it is unresponsive to the environment within which it lives.

Complex multi-celled organisms with specialized cells and tissues, like vascular plants, require more refined levels of regulation and, because they contain specialized cells, picture the xylem cell which add girth to a tree’s trunk the vascular structure that moves water and nutrients up from the roots, these are completely dependent on the other cells and tissues of the tree for their existence.  The tree, the community of cells that comprise it, must remain healthy and vital so that the many other specialized cells can do their job and the various specialized xylem cells can continue to receive the nutrients and water that they require. 

The complex structure of a plant’s leaf, contains many more specialized cells that are all required to be in correct relationship with one another.  The leaves form from meristematic tissue, grow to a prescribed shape and size, perform their function and then at some point, are shed to be replaced by others.  Cells don’t massively multiply, they grow in correct association.  A leaf grows into a prescribed shape and size.  But this was not always the way.  At least one ancient, but still extant species, Welwisczia can live for hundreds of years yet only ever has the same two leaves they begin with that never cease growing, indeterminate.  The two leaves apexes gradually dry and shred as their tissue is replenished from their bases.   There have been many possibilities.

Plants require minimum levels of CO2 for photosynthesis and of O2 for respiration.  Green plants photosynthesize producing energy rich compounds, carbohydrates, that they can later use to metabolize, releasing the energy stored in their chemical bonds to power their internal functions as needed.  These necessary metabolic functions include producing various compounds, proteins, hormones, enzymes and catalysts  within their organelles from the soluble nutrients available to them in surrounding water, dissolved, diffused into it from the adjacent soil or water.  Utilizing the energy held within the chemical bonds of these carbohydrates, plant cells, produce the energy rich molecule, ATP, something animals can also do, which contain essential electrical charges within its bonds that power the cell.  Once ‘spent’ the ATP now having lost its, is sent back to a mitochondria to be recharged and thus recycled. 

Organisms do not ‘burn’ carbohydrates as a combustion engine does.  If we did, we would ‘burn’ up our own tissues as a result of the heat required to power our systems.  While birds and mammals do produce body heat as warm blooded animals, plants, fish, insects and the many microscopic forms of life here, do not.  Our warm blooded capacity is the result of an innovation, one that separates us from other life in that we are able to produce at least some portion of our own heat to maintain an optimal working temperature within our bodies, just as we have developed a variety of strategies to ‘waste’ excess heat and cool ourselves when needed, unconsciously.  So called cold-blooded animals and plants don’t do this.  They are completely dependent upon the ambient temperature within which they live.  Carbohydrates, once produced within the leaves and green stems, are transported through vascular phloem tissue to the plants many other cells for storage or use.  Once received by the cell the carbohydrate moves to the mitochondria where it is molecularly broken down.  Heat is released in this process, along with the electrical energy once contained in its bonds, but it is a relatively small amount increasing or decreasing in step with the plant’s stage of growth and the ambient temperature.  Most important here is this harvested electrical energy which goes toward recharging ATP molecules which then move through the cell to power its internal operation.  Temperature determines the ‘base’ speed of chemical reactions, including all of the biochemical one’s within organisms.  Fine tuning of this process comes from elsewhere including the use of hormones and enzymes.  Warm blooded organisms are more complex, later developments along the evolutionary path, that require more calories to maintain their ideal internal conditions.  Warm blooded organisms are able to continue their internal processes when ambient temperatures drop.  Like us, each organism has an optimum temperature range and all of them lie within a relatively narrow window related to the temperatures here on Earth and the physics of the unique molecule that is water.

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

C6 H12 O6 + 6O2 <=> 6CO2 + 6H2 O

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

<< sun light – energy >>

<< photosynthesis – respiration >>

Moving left to right this is the equation for respiration, whether in a plant or an animal…the oxidation of carbohydrate releases heat and electrical energy for use within the cell.  It is the opposite of the reaction taking place in photosynthesis.  Photosynthesis moves right to left in the above equation utilizing the converted solar energy in its bonds, ‘storing’ it.  Respiration moves left to right releasing that energy for metabolic processes within the cell.  Electrical energy.  The mitochondria within the cell converts this into the more available form of Phosphate rich ATP using its electrical charge from the broken down carbohydrate to add a phosphate ion to the spent ADP, D for diphosphate (2) instead of T for triphospate(3), which is transported around the cell and organism to power needed metabolic processes.   The ATP molecules are unstable and readily give up their charge and phosphate ions within the cell.  Cells are then entirely dependent upon having an adequate supply of phosphate ions at all times.  They aren’t consumed or excreted, they are simply passed back and forth as energy is spent. In both animals and plants extra carbohydrates are stored in starches and fats for later use.  ATP is used for immediate needs.  This is where the starches in rhizomes, roots, stem structures, evergreen leaves come from and why they are essential to the Spring commencement of growth when energy is required to create new structures beyond a plant’s capacity to produce it.  Essential to this is the water molecule whose capacities have shaped the functioning of an organism at every level.fourth-phase-water-1

Water: The ‘Magical’ Ingredient

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

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

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

When thinking about water in its fourth state it may be helpful to think of it as being bonded more densely, in a highly structured arrangement, to the water molecules next to themselves matching each of their positive and negative charges to those of an adjacent water molecule, leaving no ‘space’ for ions to bond to, resulting in a ‘cascade’ of ions…as if a light switch suddenly changed the chemical composition within the cell.  The innumerable switches that exist within an organism can switch ‘on’ and ‘off’ very quickly effecting things like muscular contraction, the release of enzymes held with in vacuoles and signaling of other individuals of a local population when an individual is under assault.  Such ‘switching’ can result in ‘pulsing’.  Fluids can be caused to move through vessels by this coordinated streaming of water and ions away from the positively charged water molecules.  In small diameter vessels this exclusion zone forms along the inner walls the charge differential creating a flow through it in either direction.  This direction can be set by some other initiator.  Water, internal fluids, can thusly be caused to move between a cell’s organelles and inter-cellularly between cells and throughout an organism.  Enzyme released from a vacuole can then be moved and trigger a shift within the cell initiating a cascade throughout a tissue.

I suspect this action, this vascular flow is what occurs in a plants conducting vascular tissues as it draws water and nutrients up through its roots to the rest of the plant and from stored tissues to respiration sites.  Flow from the roots to leaves cannot be driven by vacuum pressure alone created by the loss of water out leaf stoma, it’s simply insufficient to draw enough volume up through a plant, especially a tree, but should be sufficient to ‘prime’ the process created by the phase shift I described above.  It also goes a long way to explaining how dissolved carbohydrates can move omni-directionally from storage organs and leaves to meristematic tissues, growth buds and cambial tissue, to power and support growth.  The flow of these materials through phloem tissues has long baffled science.  How can they move this way and what triggers and controls its direction so that growth proceeds uninterrupted?  Such flows occur within the cell and throughout every organism, plant and animal…largely because of this unique capacity of water molecules.  This is a very simplistic and short description of what is going on within cells continuously on the scale of nanoseconds.

These cascades along positively charged surfaces, along protein’s, can be triggered by specific tiny changes, initiated by catalysts, produced by the cell and are dependent upon the precise composition and proportion of the ions of the intra- and inter-cellular water, inside and outside the cell.  The presence of water adjacent to a protein with the ‘excitation’ caused by certain frequencies of ‘light’ does not just switch water into this fourth phase and leave it on until the light source disappears.  As a fluid water molecules are in a constant state of motion exchanging bonds with neighboring water molecules much as dancers might in a group dance…there is a strong attraction between them to maintain contact and an equal need to move on to the next partner and these changes happen over vanishingly short time spans.  This free association is greatly reduced in both its solid, ice, phase and its fourth, denser and more highly structured liquid phase.  The exclusion zone, EZ, itself is ‘fluid’ varying in ‘depth’ as it casts off negative hydrogen ions, -H, ‘restructuring itself and ‘thickens’ the exclusion zone then shrinking the EZ as it thins phasing back into liquid bulk water. The balance of ions is critical to the functioning of the cell.  Together, the ion composition of the water, available catalysts and physical stressors, create a fluctuating charge gradient within the cell, tissues, organs and the organism itself.  A living organism is electrically charged and thus in a state of dynamic disequilibrium.  When certain ions are not available, certain functions cannot progress (There is a reason why sports drinks claim to replenish one’s depleted electrolytes).  This occurs in all living organisms plant, animal, fungi and microbial.  These shifts in phase are coordinated within the cell, tissues and organism resulting in an ‘appropriate’ response by the cell to the stress or stimuli.  (Simple, right?) Over the course of many millions of years the many relationships and functions of organisms refined and evolved in such ways that were supportive of more complex cellular and multi-cellular life, requiring that this internal communication be capable of extending beyond the individual cell, to other tissues and the organism as a whole.

Life began in Earth’s waters, for a very good reason. The bio-chemical reactions that are critical to life require water and what better a medium for this to take place in than within a body of water itself, where conditions more conducive to these reactions/ communications increase their likelihood in very simplistic organisms.  The development of the cell initiated in Earth’s waters and continued there for some 3 billion years before life moved on to dry land…and it remains central to its process today having evolved structures and strategies so that organisms can carry the water they need within themselves protected from the challenge of aridity outside of their bodies.  Terrestrial organisms still maintain essentially the same conditions within themselves as do aquatic organisms that still rely upon the water they live in.  In order for plant life to move to land they had to develop the ability to protect themselves from the desiccation that comes with aridity.  Today’s organisms still carry within themselves tiny universes of primordial sea.

All of these actions and processes within an organism and cell are enabled and supported by the qualities and capacities of the ‘stuff’ that makes up the cell, its molecules, atoms and subatomic particles.  The energy that animates life is part and parcel to the energy that animates and defines all matter.  Electrical charge, the strong and weak nuclear force, light and gravity, all play a role in this as does the physics of ‘strings’ which lay at the base of everything, strings and the energy of their vibrations, their resonance and the ‘quantum uncertainty’ within all ‘things’.  The world is not as ‘solid’ as we would like to believe.  It is in a constant state of change, of uncertainty, happening at rates beyond our comprehension as humans.  The lines are blurred.  At each level, at each increasing order of structure, from the string, to the subatomic particle, to the atom, to the molecule, to the cell, to the tissue and finally, to the organism, this is true.  The energies exhibited at each level follow directly from that which precedes it.  The energies of life do not arise magically from nothing and nowhere. 

At its most basic level this world is invisible to our eye.  At this stage in our understanding much of it is even beyond our most precise technologies to penetrate and beyond the common imagination, as it exists in dimensions beyond the abilities of most of us to comprehend.  It requires that we understand that there is much more around us than we can physically perceive and a willingness to trust in those physicists and mathematicians who are working out the pieces of this puzzle.  Many of our modern technologies are beyond the understanding of most of those who use them.  They are not magic.  This is one of science’s leading edges of research and discovery and it will require of us that we ‘let go’ of certain basic assumptions we have knowingly, and unknowingly, been carrying with us.

Further Reading:

Important, to me, in more recent years has been the writings of scientists and authors like Drs. Lynn Margulis and James Lovelock, responsible for the Gaia Thesis.  Margulis, as a micro-biologist, wrote many books and papers on the development of life and the cell over her career which are quite accessible.  Microcosmos: Four Billion Years of Microbial Evolution, Lynn Margulis & Dorian Sagan (Margulis and Carl Sagan are his parents), University of California Press, 1997, is a good place to start.  Gaia speaks to the ‘directionality’, the increasing complexity and coherent nature of life as a ‘system’, the living Earth, and how its function is analogous to a single organism.  There is a consistency in operation across all life as different as individual species may seem to be.  Margulis’ work was central to the theories of Endosymbiotic Theory or Symbiogenesis, the theory that the modern Eukaryotic cell was the result of the merger of earlier, simpler, Prokaryotic cells, of bacteria, a process that added to the cell’s complexity and functionality.

Cells, Gels and the Engines of Life, 1st. ed., Gerald Pollack, Ebner and Sons, 2001.  This is a more recent book for me.  As daunting as this may sound, this is a wonderful introduction into the inner workings of the cell written by a University of Washington professor of bio-engineering with a gift for putting the technical into very accessible layman’s terms.  It is still not a quick read, not because of its jargon..but because there is simply so much that is new for us to grasp.  Here is a link to his lab’s website that continues to research the properties of water.  At the time I wrote this I had yet to read his other book, The Fourth Phase of Water: Beyond Solid, Liquid and Vapor, Gerald Pollack, Ebner and Sons, 2013, which I now own and would include on a must read list for anyone,  It is quite accessible and explains many phenomena we come across every day.

Living Rainbow H2O, by Mae Wan-Ho, World Scientific Pub., 2012, looks into the essential role of water in the processes of life…recommended!  This is the first book I read suggesting that water played anything beyond an auxiliary and neutral role in life and the cell.  These ideas are relative new to science.  Previously water was viewed as ‘just’, a unique molecule, but still limited to a less active role as a carrier, and solvent with a few unique characteristics such as the range of temperatures across which it is liquid, its expansion to a less dense solid crystalline structure when it freezes, its strongly di-polar nature which contributes to its qualities as a solvent, a carrier of charge, and both its tendency to cohere to itself and adhere to other bodies.  Wan-Ho was a geneticist working in the UK who became very interested in the physics of the organism later in her career.


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