Category Archives: Plant Metabolism & Photosynthesis

Physics, Evolution, Natural Selection and the Generative Power of Far Out of Equilibrium Dissipative Structures (Organisms), part IV; An Annotated Bibliography of Some of My Sources  

Al-Khalili, Jim and Johnjoe McFadden, “Life on the Edge: The Coming of Age of Quantum Biology”, Broadway Books, 2016. In the world of science, quantum biology is a toddler.  Quantum mechanics itself only began a hundred plus years ago and quickly began reinterpreting the way that physicists look at the world.  Today most branches of science are transforming themselves aligning themselves with this new reality of physics.  This maybe impacting none of the sciences more than it is biology and the life sciences.  What was once limited to the quantum world of elementary particles much smaller than we can see even with technology’s assistance, today we are finding quantum actions behind even the most simple processes up to and including the energy and origins of life.  Mass and energy lie at the heart of everything and life is a very particular case of highly complex ordering of that mass and energy, intricately linked in coherent relationships, borne out of seemingly random, chaotic, actions at a subatomic level.  In these systems/organisms life has evolved effective patterns that ‘feed’ on themselves, self-regulating, self-maintaining, able to reproduce with great ‘fidelity’ to one’s parent organisms, energy dissipating structures, dynamic, balanced between stasis or death and a runaway consumption of one’s self,, a conflagration.  Patterns built on more basic patterns, conformed into very particular resonant structures which are additive and transformative, never perfect, evolving towards greater complexity and capacity, structures that ‘live’ in relationship to one another in a supportive manner, dynamic, time limited and ‘stable’ in a self-reinforcing sense…existing in different states, simultaneously.  Follow Al-Khalili and McFadden down part of a ‘proven’ path. Continue reading

Physics, Evolution, Natural Selection and the Generative Power of the of Far Out of Equilibrium Dissipative Structures (Organisms), part 1

On Darwin and His Theory

Evolution is a word that can divide the world.  Its opponents often claim that all that lives today, in terms of species diversity, did so yesterday…all the way back to the ‘first’ yesterday, which some people claim was precisely 4004 B.C., when ‘God’ created everything essentially in a moment.  Bishop Ussher, of Ireland, published his ‘findings’ in 1650 and his ‘documentation’ is that most frequently referenced by opponents of evolution.  He has it down to the day, Oct. 23 of that year.  This is a problem when a researcher goes in with an ‘answer’ and is only looking for corroborating evidence, evidence which they will eventually find.  Science, through the study of evolution, has developed various specialized technologies and techniques to reach back in time and analyze the evidence at hand.  It has done this building on the work of those studying paleontology, microbiology, geology, chemistry, atmospheric chemistry; palynology, the study of pollen; astronomy and cosmology, quantum physics, stochastic methods developed around the hypothesis of a molecular clock which posits a rate of genetic change; and cladistics which assesses genetic lineages, the relationships between species and larger classification groups…scientists have collectively been dating ‘life’ back over Earth’s 4 billion years.  The creationist argument depends entirely upon belief, denies science and views evidence such as fossils simply as ‘puzzles’ God left to confuse us.…Others accept that lower species may have ‘evolved’, but Man, created in His image, is special, exceptional and exempt, a creation of God, fixed and forever.  Modern science does not give a pass to such claims of specialness seeking instead more direct evidence, making connections, following patterns, doing science….

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The Flowering of Monte: Going ‘Viral’ During a Pandemic


When will it actually flower?  Once people got passed the, ‘What is ‘that’ question?’, this is what they wanted to know.  When would it actually flower? by which they meant the individual petalous flowers open.   More than a few times I responded snarkily…it’s flowering right now!  Agave are among a wide ranging group of plants whose flowering includes a relatively large inflorescence, a supporting structure, which can rival the rest of the plant in terms of size.  An Agave montana flowering here is foreign to our experience.  The idea that such a large structure  could arise so quickly, is to most people’s minds, strange, if not surreal…but for experienced gardens, who observe and strive to understand, there are links and connections, shared purpose and processes with all flowers.  Gardeners and botanists, horticulturists and evolutionary scientists, they see the wonder in it all.  When does flowering begin?  When a plant commits to its purpose.  Flowering should not be taken for granted.  It does not occur to meet our aesthetic need.  It is also much more than a simple result of a plant’s life.  It is a fulfillment of one well and fully lived, projecting oneself into the future.  Flowering and the production of one’s seed is a commitment to a future that will go on beyond oneself…and it begins from where every plant begins. Continue reading

Viruses in Plants: Life, Disease and Evolution

Gardening for most of us is more than just a distraction, but these days, in light of the coronavirus, SARS-CoV-2, the disease it causes, COVID-19, the conflicted messaging we’re getting from our ‘leaders’ and the insecurity many or most of us are feeling around our own financial situations, we are likely more in need of one than we had been. This post will be a bit of that, while at the same time an attempt to shed a little light on the issue of viruses in the plant world. Yes, viruses plague plants as well, but they are also thought, by more than a few scientists, to have played other roles as well, such as in evolution, a process that continues to and beyond this day! In some ways they parallel those of bacteria. Both viruses and bacteria can cause disease. The disease that a virus can cause is generally very limited to a narrow range of species, even to one, with notable exceptions. Most, however, perform other tasks as they go about their ‘business’, within the bodies of bacteria and larger multi-celled organisms. In fact most viruses, like bacteria, play no direct roll in our health…and they are everywhere.

It is important to understand that science has its own biases and that our perspective as mortal human beings affects how we view things as well…viruses included. Science builds on experience. It requires that new science, and its theories, be consistent with what is ‘known’, but it must also be open enough to avail itself to new understandings when it better explains previously accepted theories. What do I mean? Viruses ‘cause’ disease, but might they also be something else? If our biases set us up to see them agents of disease, reservoirs for future disease or inconsequential, we will fail to see what they may also be…and there are some who would assign a much more important role to viruses and see them not just as disease agents, but as far more, as essential ‘elements’ and players to life today and the processes that made today’s form of it even possible! First, though, what do we ‘know’ of viruses. Continue reading

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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Latitude and Energy: A Beginning Point

45º!  In my previous post I suggest, for reasons of solar gain and intensity, that we gardeners might have better luck choosing plants for our gardens if we chose them from our own latitude, north and south.  The intensity of the sun’s radiation varies with latitude, decreasing as we move away from the equator toward the poles.  Like all horticultural suggestions you should take this with a grain of salt…er, soil.  Follow that line around the Earth from Portland and you can run into a lot of difficulty.  Spin a globe and take a look.  Following the 45 parallel east takes us along the Columbia Gorge, across the Blue Mountains, Hell’s Canyon, the resort town of McCall, Idaho, elevation one mile, the Frank Church River of No Return Wilderness and more of the Rockies, on across the northern Plains, through South Dakota, Minnesota, Michigan, our ‘frozen heartland’ and east through New York and just outside Portland, Maine.  These are highly varied landscapes with conditions almost always colder, different rain patterns, more extreme weather conditions than ours with corresponding plant communities.  In Europe 45º passes through northern Provence, with weather strongly influenced by the adjacent Mediterranean Sea and the massive Sahara Desert that lies beyond, the Piedmont region of Italy, Croatia, the Black Sea, the Steppe country including Uzbekistan, into northern mountainous China and southern Mongolia and finally, the Japanese island of Hokkaido, its capital, Sapporo, a couple degrees south, with its remarkable annual ice festival. 

The list of landmarks found along the southern 45th is very short, as the vast majority of its length is defined by open ocean.  Still it crosses New Zealand’s South Island, only again making landfall in the south of Argentina where it narrows down toward the continent’s southern tip and the Chonos Archipelago of small Chilean islands comprised of submerged mountain tops.  On the later the landscape is dominated by compact cushion plants.  These few places have strong maritime influences and are much effected by the unimpeded weather sweeping off of Antarctica.  Much of this sounds limited and extreme when I think of plants adapted for our region. Continue reading

Here Comes the Sun: Latitude and its Seasonal Effect on Life and Place

Read to the Beatles, “Here Comes the Sun.”

It’s a bright sunny morning here in Portland…in January, not a real common occurrence in a place where we typically have some kind of cloud cover due to our climate with its strong maritime influences…but today it is sunny, and I’m thinking about the annual cycle of changing day length as we move from our shortest day, on the winter solstice, toward our longest day, on the summer solstice.  The solstice result from the tilt of Earth’s axis, which remains more or less fixed, though there is a bit of a ‘wobble’, as the Earth follows its annual orbital path around the Sun, spinning like a top, effectively changing the surface it presents along the way. Continue reading

Agave montana: Monte’s Flowering Attempt…and What’s Behind It

It’s October in Portland and my Agave montana is in the process of flowering…I know, we’re heading toward winter, with its rain and average low down into the mid-30’s with potentially sudden damaging temperature swings from mid-November into March dropping below freezing to the low twenties, with extremes some years, generally limited to the upper teens, though historically, some areas have dropped into the single digits, those Arctic blasts from the interior….Winter temps here can be extremely unsupportive of Agave’s from ‘low desert’ and tropical regions.  Combined with these cool/cold temperatures are our seasonal reduction in daylight hours and its intensity (day length and angle of incidence varies much more widely here at 45º north) and the rain, ranging from 2.5″ to 6″+ each month here Nov.- Mar., resulting in a ‘trifecta’ of negative factors which can compromise an Agave, even when in its long rosette producing stage.  Any Agave here requires thoughtful siting with special consideration for drainage, exposure and aspect.  For an Agave, conditions common to the maritime Pacific Northwest are generally marginal, yet I am far from alone in my attempts to grow them here.  Previously, in April of 2016 I had an Agave x ‘Sharkskin’ flower, a process that spanned the summer months, taking 7 until mid-October to produce ripe seed.  I was initially a little pessimistic this time about A. montana’s prospects.  Why, I wonder, if plants are driven to reproduce themselves would this one be starting the process now? Continue reading

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.   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