Category Archives: Botany

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.
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

dicot-seed

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

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! ]

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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, 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