Category Archives: Botany

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.
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

Passing the ‘Baton’: On Life, Seeds, Germination and Vegetative Propagation


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,

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

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

An Introduction for Gardeners to the Eudicots and the New ‘Phylogeny’ of Angiosperms: Genetics and the APG, Part 1



While working on a blog posting over the spring of ’17, Palms, Bananas, All Monocots…Oh My! Their Similarities and the Differences that Distinguish Them From Dicots…and why this should matter to you! discussing Monocots, I necessarily said much about Dicots, those vascular, seed producing, Angiosperms (flowering plants) with two cotyledons or ‘seed leaves’.  These were the two major groups of Angiosperms that I grew up with in the gardening world…but, while I was working in my career, this began to change, beginning  some 25 years ago.  I’d been aware of the term Eudicots, or ‘true’ dicots, and knew that all Eudicots also fit within the older category of Dicots, while a small portion of the latter, are left outside.  I was unsure how these differentiated and so, ignorantly (not a bad word), blurred the two together as many have been doing since the concept of Eudicots was first put forward.  The differences between these two for me seemed very ‘arcane’ and fussy, focusing on the tiny pores or furrows, colpi, on pollen grains.  But it is more than just that.  To really understand what is going on in the esoteric world of taxonomy, the naming and organizing of plants and their relationships to one another, you need to look at the genetics, the DNA ‘fingerprints’ of a plant which allows us to follow evolutionary paths back from the plants of today through their ancestors to the earliest forms of life on Earth.  It is about the phylogeny, the ‘history’ and relationships that tie plants together. Continue reading

Puya: Growing These Well Armed South Americans in the Pacific Northwest

[I wrote this originally about 2 years ago as part of what turned out to be a too long look into the Bromeliad Family.  Here I present only the genus Puya spp. in an edited form with the addition of the species Puya berteroniana.  Go to the original article to read about the shared evolution of the several genera and families that comprise the family, why these are not considered succulents and a look at the armed defenses of many plants.  My plan is to breakout at least some of the other genera as well as I think the length of the original post may have put some readers off.]

Puya: one of the Xeric Genera of Terrestrial Bromeliaceae

The name “Puya” comes from the Mapuche Indian word meaning “point” (The Mapuche people are indigenous to Chile and Argentina.  They constitute approximately 10% (more than 1.000.000 people) of the Chilean population. Half of them live in the south of Chile from the river Bío Bío to Chiloé Island. The other half is found in and around the capital, Santiago and were mostly forced to the city after Pinochet privatized their lands giving them to the wealthy.)…the assignation is clear and the pointed, spiky, nature of this genus is immediately obvious to anyone.  But there is something easy and comfortable about the sound of the word in your mouth when you speak it…poo-‘yah.  Puya are native to the arid portions of the Andes and South American western coastal mountains.  (Oddly, two species are found in dry areas of Costa Rica.)

Puya spp., populate arid western regions of the Andes Mountains up into southern Central America.  These are terrestrial plants, relying on their roots to find the moisture that they need.  They possess the same basic rosette structure common to all members of the Bromeliad family to which they belong, including their petiole-less leaves, which clasp directly to a compact stem structure, funnelling the infrequent, and seasonal, precipitation they get into their crowns and root structures where they can take it up, a strategy very similar to Agave and Aloe which grow under similar conditions. Continue reading

Ginkgo biloba: on reproduction, evolution and anomalous existence

There are six Ginkgo trees here along Main St., on the north side Chapman Square, downtown, they are the most abundant species on the two blocks and the smelly not-a-fruits that drop in the fall demonstrate that many of them are female.. You can see the Elk fountain, one of several fountains once installed so locals could ‘water’ their horses. Only two the Ginkgos on the two blocks are male clones that I know of, the others are a mix of male and female seedlings. The male strobili are still in evidence on the trees. The female trees appear to hold their strobili on higher branches, as I could see nothing on the available lower branches with my bad eyes.

Mid-April and the Ginkgos are flowering….well, technically not ‘flowering’, because they aren’t angiosperms.  Botanically speaking, they are doing what they do instead, forming the little structures that contain their sex organs for what would most likely be failed attempts at reproduction.  Think about it, in a community filled with males no progeny will be produced.  We were on one of our walks down an inner section of Tri-Met’s Orange Line, approaching the Tilikum Bridge, when I noticed this event…I was a little surprised.

If you know much about Ginkgos you probably know about their fruit, which again is not technically a ‘fruit’.  Only angiosperms, true ‘flowering plants, form ‘fruit’.  The Ginkgo’s ‘fruit like’ structures are notoriously stinky when they become ripe, smelling like what many describe as being similar to dog ‘poo’, others liken it more to ‘vomit’, either equally unpleasant, when they fall to the ground and splatter or are stepped on…one of the reasons why these trees are cloned, grafted, by the nursery industry….By cloning selected forms propagators allow us to remove the chance of purchasing a female tree…unless in their zeal to bring a particular form to market they select a tree that hasn’t flowered yet….Without looking at their chromosomes, it is nearly impossible to determine the sex of a juvenile tree.  Clones stay true to their sex, so if their scion wood, or buds, are taken from a male tree, the result will be a male clone.  Ginkgos are a dioecious species, ‘di’ meaning two, so any one individual plant produces only male or female structures, so it takes two trees, of opposite sex, to produce viable seed.  Monoecious means that an individual plant produces male and female structures.  In Ginkgo spp. and the non-flowering gymnosperms these sexual structures are called stobili or singularly, a strobilus. Continue reading

Fabiana imbricata: the Andean Un-Tomato, a Non-Heath That Looks a lot Like its Cousin Cestrum


Fabiana imbricata has an appearance much like the upright and shrubby Erica arborea…maybe mixed with an upright form of Rosemary…providing a remarkable texture in the garden.

In gardening and botany one of the first things we learn is that not everything looks as we might expect that it should!  Fabiana imbricata, is a member of the Tomato Family, the Solanaceae, yet, if you don’t look too close, it looks like it might belong to the Ericaceae.  At one time I was planning to take advantage of this similarity as I was attempting evoke a South African feel in part of my garden substituting this for one of the many tender South African heaths as the correct Erica species are either too tender, of borderline hardiness for my conditions or are simply difficult to come by.  It was sharing an area in the garden with Restio capensis, Eucomis spp., Melianthus spp. and others to give an impression of South Africa, not a strict species for species duplication of a community.  I didn’t quite pull it off….I’ve done much the same thing when substituting tropical looking temperate plants for the real thing when evoking a tropical feel.  It’s a matter of manipulation…a sleight of the garden hand.

Its Chilean Home and Garden Merit

Fabiana imbricata is not from South Africa, though it shares Gondwanan roots, and is endemic in Chile, occurring very frequently throughout much of its Andean range.  It is in fact identified as a ‘keystone’ species strongly effecting the composition of its local plant communities.  It can be found growing from well into the dry region of Coquimbo in the north, just south of the huge Atacama Desert, south into the wet Aysen region with its many islands and inlets south of the Lake District or Zona Sur.  The vast area stretches along much of Chile’s length which can be driven, on often tortuous mountain roads, for over 1,700 mi., stretching from the arid city La Serena to the small, rainforest town of Tortel, in the south, a distance almost 500 miles further than the drive from Vancouver, BC to Los Angeles, CA….There are not that many plant species in the world that span a similar latitudinal range with its accompanying climate differences.  As you look for this plant moving from north to south through Chile, the soils and its particular niches change along with the temperature and rainfall.  You are more likely to find this growing exposed in rocky scree in wetter regions to the south, while it tends to be more commonly found on sites more protected from the sun’s intensity and into better soils as you move into the arid and hotter north, more protected from the sun’s tropical intensity.  No surprise there, but overall this is an adaptable plant succeeding in cool rainforest to arid, desert like, conditions.  As would be expected across the more arid portion of its range fire is an important factor in maintaining the plant communities balance, riding it of other competing woody plants  and even aiding it in germination, when followed by ample winter/spring rainfall, though this is obviously not essential for its continuing survival in rainforest areas where fire is much less frequent.   This is a very adaptable species and as we live near the Pacific Coast in the northern hemisphere, which mirrors much of the range of conditions, we should be able to have success with it, if we pay attention to its cold limits.  Those away from the Pacific Coast, especially those with ‘continental’ climates or strong influences from them, will have to pay closer attention. Continue reading

The Fascicularia and Ochagavia Question: Two Worthy and Relatively Hardy Bromeliads


The inflorescence of Fascicularia bicolor with its blue flowers. The center of the foliage on a blooming rosette, turns red when the flowers appear and then, like many Bromeliad, that rosette dies replaced be previously formed offsets. My blooming plant had multiple rosettes at the time, three of which bloomed. Taken in my garden, Sept. of ’17.

If you’re not into blood and guts, consider this genus, as on my scale of one to ten as described above with ten warning of near complete evisceration if one is fool hardy or reckless, this one’s a solid 4, dangerous enough but not stupidly so.  Fascicularia pitcairniifolia.  You would think that in a genus composed of one or two species things would be pretty well settled taxonomically, guess again. Originally described as F. bicolor it was reclassified as F. pitcairnifolia and later changed back to F. bicolor.  Subspecies were proposed.  Changes retracted.  There are significant differences in the sampled populations, but were they sufficient to constitute separate species??? Adding confusion at a different level are those who say the species name indicates that it is from Pitcairn Island.  It is not.  The specific epithet simply recognizes a similarity to the foliage in genus, Pitcairnia, another Bromeliad member.  This Fascicularia is from the lower Chilean Andes, allegedly north of the other Fascicuaria species, F. bicolor which is suppose to be slightly hardier and occurs at least occasionally as an epiphyte!  Some botanists have argued that F. pitcairnifolia possesses thicker, slightly wider leaves. and some minor differences in the timing of flowering and is reputedly slightly less hardy.  The ranges of both overlap  Good luck sorting this out. Continue reading