Category Archives: What is Life?

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

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

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

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

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

….This might be a good place to take a break…then reread the above.  The reader might do well to take this approach as your ‘work’ your way through this, bit or bite by bite.
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Passing the ‘Baton’: On Life, Seeds, Germination and Vegetative Propagation

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This diagram is of a typical bean seed here to illustrate some of the basic structures within all seeds. When germination begins water is taken in via the Micropyle. This picture is taken from a simple introductory page, https://byjus.com/biology/identification-of-the-different-parts-of-an-embryo-of-a-dicot-seed/

EVERY, let me say that again, every, single individual organism, plant, animal, fungi and bacteria…is directly linked, in an unbroken line, to previous organisms.  An organism is not created singularly and anew within a Frankensteinian lab, whether of our own hand or nature’s.  Life is an extremely rare occurrence.  Genesis did not happen, in the biblical sense, but on extremely rare occasions, arguably only once in Earth’s several billion years.  The conditions it requires are unique, precise and stable.  Just as individuals are linked directly to their parents, entire species are to their predecessors.  So called ‘spontaneous generation’ does not happen.  The idea that organic matter can be manipulated and ‘sparked’ into life is naive.  It can only be more or less manipulaed as we’ve demonstrated time and again in a heavy handed way.  Science, especially over the last one hundred years, has made great strides in understanding just what life is, what it requires and how it most likely evolved, but it still cannot ‘create’ it.  Even in its most simple forms, such as bacteria, life requires the ability to conduct thousands of biochemical processes within each cell in a very precise way, something that not even a series of highly coordinated human operated laboratories, using standard of the art equipment, can do in anywhere near the amounts and efficiencies that a single living cell can.  We are far too clumsy.  Doing this for a complex multicellular organism with highly specialized cells, tissues and organs would seem impossible.  As we continue to study organisms, their processes and growth, we are learning just how complex and astounding they are. Continue reading

The Basic Code of the Universe: The Science of the Invisible in Physics, Medicine and Spirituality – A ‘Discussion of Ideas’

A1SRgFYkq3LThe Basic Code of the Universe: The Science of the Invisible in Physics, Medicine and Spirituality, is not an ‘easy’ read…such should be expected when a book challenges not just our understanding of the world, but even the accuracy of our perceptions of itI  This is leading edge thought in the sciences today coming at a time when the basic precepts of science are being called into question by the political and religious right. The last several decades have seen an accelerating rate of scientific advancement at the same time that the general public’s understanding of it is dropping ever further behind.  Today while advocates press to re-emphasize STEM (Science, Technology, Engineering and Math) in public education, another segment has been working in opposition demanding a return of public education to the ‘3 R’s’, in keeping with the ‘fundamentals’ of Christian conservatism.  This vocal minority rails against our acceptance of a science that questions their ‘world view’ arguing that science’s ‘valueless’ methods poison our ways of thinking raising doubt, putting people in conflict with their basic beliefs and the dogma they espouse.  These people question science’s relevance and wish to look no further than the fundamentalist thought of their religion.  Such doubt and rejection should be raising red flags around the world as people, drawn to their own ‘righteous’ paths, find themselves increasingly in conflict with others on their own separate path. 

I, myself, have always been drawn in many directions, fascinated by one topic then another, but over time forming a rather comprehensive overall interest in the world…more wholistic.  I will never become ‘expert’ in one thing, finding life and our place in the universe endlessly a wonder!  So, I find myself drawn into such topics as evolution, quantum biology and the physics of life, fleshing it out with studies into the particularity of place, places like South Africa, Chile, the Canary Islands and our own Pacific Coast region of North America, with their particular geologies and living communities.  I find the ‘big questions’ the most interesting and will sometimes put considerable energy into trying to understand their possible ‘answers’.  I ‘intuit’ and combine, finding that our world has been so committed to the narrow and fractured views of our countless experts that our understanding of the world and our place in it has become ever more ‘confused’…so again, I am drawn to this and books like this. Continue reading

Death and Life in the Garden: Learning in the Garden Classroom

As gardeners our hands are ‘bloodied’ with the chlorophyll of plants…while it may not stain us as ‘murderers’, we are never the less complicit in their deaths…as much as we are necessary for their lives.  Without us, as a group, these garden plants would never would have been propagated and, if not for our ‘selfish’ acts in the garden, choosing, designing and displaying them, many would be passing into obscurity, most of us knowing nothing of them or of their loss, their passages into decline and extinction, even more quiet, unnoticed, as too many already do today.  While we may acquire and attempt to grow them with the ‘best’ of intention, eventually, they will all die, ill fit or not, suddenly or after many years in our gardens, as a result of our ignorance, impatience, simple curiosity, our desire for something ‘different’, or even in spite of our best informed efforts.  Death comes to all things and our gardens are no exception.  Our gardens art artificial after all, creations of our making and they do not comprise a viable population that will out live us, reproducing in place, making the adjustments that they must over time to survive.  To do this would take an unprecedented amount of effort and coordination on our part and that of our neighbors.  The setting of our gardens are unique to us and their purposes are much narrowed and more intentional than are the places their progenitors come from, the ‘gardens’ of their origination.  For many of these plants our relationship with them might best be thought of as student to teacher as nature sacrifices itself in an attempt to teach us of what is being lost, ever since we stepped out of the loop that once put us in daily direct contact with nature and came to embrace this modern world and its expectations of consumption, ‘ease’ and never ceasing growth…so it is not ‘murder’, it is life, an attempt to return and reclaim.  There is purpose to be found in our gardens, well beyond surface amusement and distraction in what is too often becoming an ever uglier world, or for some of us our need to impress in a game of one-upmanship.  Nature demands more of us, that we accept our role as student and become careful observers, willing acolytes…maybe even crusaders….Too much? no, I don’t think so. Continue reading

Evolution, Speciation and What it Means to the New Phylogeny: A Primer for Gardeners, Part 2

 

 

Understanding the New Phylogeny of Angiosperms, part 2

We tend to think of evolution as a historical process, something that occurred in the past which has resulted in life today, with us at the pinnacle.  Humans with our opposable thumbs, our relatively high ratio of brain to body mass, our consciousness…our souls, we often argue, are the ultimate life form.  We have a hard time imagining that this is not the case, that we as a species, are a part of a continuing process, that some day will fade from the Earth, as other species, more evolved and complex, develop.  This is what happens to organisms over seemingly impossible long periods of time. It has happened and is still happening to plants.   It won’t happen today or tomorrow and this doesn’t mean that what we are or what we do doesn’t matter…because in evolution…’everything’ matters. Continue reading

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

[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.  This first ‘installment’ concerning life within the cell, is divided into two parts, the first covers the function of the cell itself and, importantly, the role of water in the cell.  The second, part 2, 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 of understand and classify plants, I found it necessary to better understand these other topics, what it is that we are ‘messing’ with! ]

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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, 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 of life in effect on our little pieces of ground and the Earth.  They reflect our understanding of the limits and possibilities at work here.  The better that we understand this the ‘better’ our gardens will be, the more in synch they will be with life.   Continue reading

What is a Species?

Specious (?) Speculations on Species 

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Iris x pacifica ‘Tanus’.  This is a hybrid Iris of species know collectively as series ‘californicae’, a group of Iris endemic to the Pacific coast of the US, primarily California, some very localized, with several occurring north through Oregon, and one, I. tenax, all of the way to the Puget Sound area of Washington.  These species obviously can be crossed.  Their form shows the distinctive tri-partite structure of a classic Monocot, in Genus Iris taking this particular form with 3 ‘falls’, 3 stamen and stigma structures angling out from the ovary at center, across the brightly colored ‘signal’ on each fall and the 3 more upright ‘standards’.

I do not recall from high school biology how an individual species was defined to us in our text or class, nor do I in my college Zoology 200 series.  All that I have is a general understanding that it is a select population with a shared, narrow, range of physical characteristics, in the case of plants, best determined by their floral or reproductive parts, that is able to reproduce stable offspring with the same range of characteristics.  Webster’s defines species as:

“a category of biological classification ranking immediately below the genus or subgenus, comprising related organisms or populations potentially capable of interbreeding, and being designated by a binomial that consists of the name of a genus followed by a Latin or latinized uncapitalized noun or adjective agreeing grammatically with the genus name” Continue reading

This Life: A Memoir, Gambol and Botananomical Tale

Sharpless 249 and the Jellyfish Nebula Image Credit & Copyright: Eric Coles

Sharpless 249 and the Jellyfish Nebula, Image Credit & Copyright: Eric Coles

 

I hope that you will forgive me this departure into verse, prose, whatever this is…another thread in my life.  I don’t think it is too far amiss, because, after all, horticulture is the ‘art’ and science of growing plants.  Originally I began this as an idea for a children’s story, yes I did, the life of a particular Dandelion, but, probably due to my more recent reading on topics like photosynthesis, cellular metabolism and a biophysics response to the question of, ‘What is life?’…it has morphed…considerably.  When you read this, keep in mind that my intention was to write from the perspective of the Dandelion, a concept pretty incomprehensible to a modern American. 

The Taraxacum Cycle

Stories all begin with a single word, a seed, around which they grow, nurtured over time by the things we all share in common, family, history and experience.  They contain ‘truth’, but are not themselves true, because they must be told in such a way that they lure the reader in and are ‘believable’.  They are organic and grow within us and to the extent that they reflect our own ‘story’, that they meet our expectations, we stay with them and them with us, because there is no story if it is forgotten.  So, the author must manipulate what he knows, he must ‘lie’, to bring you in and keep you, weave truth and lie into a whole.  We take the stories you already know and introduce our own characters, set them in exotic though familiar settings, and, if a writer is good, introduce enough, but not too much, that is ‘new’, different from your cultural experience, your expectation, that you are affected by its unfolding, that you become a part of the story and look at your world in a different way, even if only a little bit.  The word here is Taraxacum. Continue reading

The Strength to Stand: Surviving the Load of Ice and Snow in Portland

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The morning after the big snow along the front of my house. To the left, splayed out and weighted down, is my Butia capitata. This one, from Argentina and not used to snow, had me worried, but it sprung back. The Oleander to the right, next to the sign, was bent down to the ground from its 8’+. Further back is one of my Chinese Windmill Palms, Trachycarpus fortuneii, bent under a snow load it is used to from high in the mountains of southern China.

Many of us who garden in the Pacific Northwest, and especially those of us in Portland this year, will be visiting our garden centers and favorite nurseries this spring and summer with a little more anxiety and need as we look for plants to replace those that have succumbed to this winter’s cold, ice and snow loads, all of which were more severe than what we have come to expect here.  But before we pull on our boots and don our rain gear to head off for shopping there are several questions that we need to consider before we make our purchases.  Not all of us draw up plant lists, but most of us at least carry in our heads a wish list of plants we have seen in other gardens, in magazine spreads and while on vacations, but if we want to avoid some major mistakes and move our gardens toward the kind of landscapes that we really want, we are going to have to put on our reality goggles and critically assess our choices…that is, if we want to avoid unnecessary losses in the future. Continue reading