Category Archives: Growth

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

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

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

Agave colorata and its Blooming Attempt in ’18

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Agave colorata before flowering initiation, growing nearly horizontal, with a broadly cupped lower leaf holding water. From the Irish’s book, “Agaves, Yuccas and Related Plants”, “The leaves are 5-7″ wide and 10″-23” long [mine were all at the small end of this range] They are ovate ending in a sharp tip….The leaves are a glaucous blue-gray and quite rough to the touch. The margin is fanciful with strong undulations and large prominent teats of various sizes and shapes. A very strong bud imprint marks the leaves, which usually are crossbanded, often with a pink cast [not mine], and end in a brown spine 1-2 in. long.

This is one of the first Agaves I ever grew. Pictures on line of its rosette first caught my
interest, their leaf color, substance and sculptural qualities, the margins of its broad, thick leaves, with their rhythmic rounded ripples, each tipped with a prominent ‘teat’ and spine. This is not a large plant, typically growing 23″- 47″ in diameter and my plan was always to keep it in a pot as it is from coastal areas of the Mexican state of Sonora, found sporadically in a narrow ‘band’ south into Sinaloa.  Agave colorata is very rare and uncommon in nature and growing on steep slopes of the volcanic mountains in the coastal region in Sinaloan thornscrub. It often emerges from apparently solid rock cliffs sometimes clinging high above the water below.

Growing in Sonora and at Home

It is poorly adapted to our wet winter conditions though it is reputedly hardy into USDA zn 8, or as low as 10ºF.  Its natural northern limit is thought not due to cold, but by excessive aridity in the northern parts of Sonora.  I didn’t test it, leaving it outside under the porch roof, bringing it in when forecasts called for below 20ºF, as any plant is more susceptible to cold with its root zone subject to freezing. With perfect drainage and overhead protection, you might be able to get away with this in the ground, but the combination of significant wet with our cold is likely too much…still if someone wanted to try….At best I suspect this one would still suffer from fungal leaf diseases, disfiguring the foliage.

This is usually solitary, but it can be found occasionally in small clumps/colonies up to nearly 10′ across, pushing up against each other on their slowly growing and short ‘trunks’ to 4′ high.  My plant produced just a few pups over the first third of its life.

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I wanted to include a climate map of Mexico. This one utilizes the classic Koppen system designating the various climates based on temperature and precipitation and their seasonal patterns. Here it has been modified by Mexican climatologists to better reflect Mexico’s complicated geography…even so, because of the abrupt changes in elevation, and land forms, different climatic conditions can occur in close proximity to one another. Mountains can create wetter and drier areas that on a map of this scale are lost.

Sonora has three distinct geographic areas all running along a ‘line’ from the northwest toward the southeast, the Gulf of California and its associated coastal landscape paralleling the Sierra Madre Occidental, sandwiching plains and rolling hills in the middle.  The coast and plains/rolling hills are arid to semi-arid, desert and grasslands, while only the higher elevation of the easterly mountains receive enough rain to support more diverse and woody plant communities, scrub and Pine-Oak forests.

This map comes from the Arizona Sonoran Desert Museum. The link takes you to one of their pages which discusses the natural history of the desert, thornscrub and tropical deciduous forest of Sonora.

This region also varies north to south, the climate drying as you go north into the Sonoran Desert.  Moving south on down into Sinaloa, and further, is the some what wetter ‘dry deciduous forest’ biome with an array of woody leugumes, including several Acacia.  Agave colorata resides in the transition zone in between, in the portion of  ‘thornscrub’ near the Sonoran/Sinaloan border.  North and south the Thornscrub itself changes in composition.  The Sinaloan Thornscrub serves as a transition zone between the desert and the slightly wetter, taller growing, Tropical Deciduous Forest that continues the south.  All along this band running north on into Arizona’s Sonoran Desert are various columnar cactus a food source for Mexico’s migrating nectarivorous bat species.  It is a unique flora community, containing species from bordering floral regions and other species unique or endemic to this transition zone itself.  The area continues to be under threat, primarily by cattle ranching that moved into the region in the ’70’s and ’90’s bringing with it clearing and the introduction of non-native and invasive Bufflegrass, Pennisetum ciliare, also known under its syn. Cenchrus ciliaris, for pasture.  Bufflegrass is also a serious problem north into Arizona.  In Sonora many of the cleared woody species have since begun moving back in, while the smaller, more sensitive species have not.  Climate change promises to further squeeze it. (The World Wildlife Fund maintains a website with good descriptions of many eco-regions I sometimes find it very helpful when trying to understand the conditions of a plant I’m less familiar with.)

When growing plants like this, one should keep in mind the concept of heat zones.  The American Horticultural Society has created a map of the US delineating its ‘heat zones’.  It is based on the average number of days an area experiences temperatures over 86ºF.  At that temperature most plants begin to shut down their metabolic processes…they slow their growth.  Check out the AHS map (AHS US Heat Zones pdf.) and keep in mind that we are warming up!  The AHS map has us, Portland, OR, in zone 4, meaning we experience 14-30 days with highs over 86ºF each year.  Last summer, ’18, we actually had a record 31 days over 90ºF!  Now consider that the coastal/plains region of Sonora likely experiences between 180-210 such days!  Agave colorata may not need this, but it is certainly adapted to such a level of heat stress.  Something to think about, especially when you consider that we receive the bulk of our rain over the winter when our daily highs and lows average for Nov. 40º-53º, Dec. 35º-46º, Jan. 36º-47º, Feb. 36º-51º and Mar. 40º-57º…keeping in mind that we could freeze on most any of those dates.  The Sonoran Desert receives its minimal rainfall in a summer/monsoonal pattern….This is why bringing such ‘low desert’ plants to the Pacific Northwest can add another degree or two of difficulty to your success!

 

Growing this in a pot made perfect sense to me, but every decision carries consequences, not all of which I anticipated. Most Agave don’t form a ‘trunk’ growing its leaves, in a tight spiral, crowded along a very abbreviated stem, which adds little to its length to separate each consecutive leaf., but Agave colorata adds a little ‘extra’ slightly separating its leaves, resulting in a weak and kind of puny stem. If you’ve ever shuffled pots containing Agave more than a few years old, you understand that their crown, their substantial top growth, is relatively heavy, A. colorata is no exception, in fact their leaves each seem more substantial than leaves on many other similarly sized Agave. This results in a plant that as it grows begins to lean over, eventually, laying flat across the ground. As a Monocot the stems of Agave don’t caliper up over the years as does wood. These have no cambial meristem which would add secondary growth, and diameter, to the stem and as I said, with its relatively massive and heavy crown, it leans.  This is the same characteristic that gives their small colonies their height.

 

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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

On Ecology, Politics and Climate Change: the Links that Tear us Asunder

Warning!!! This is a rant! It’s political, economic, ecological and, most definitely, covers all of the connections between with climate change, these things and our future as a species.  I hope you choose to read it, but be forewarned!!

I woke up yesterday at 4:30am, unable to go back to sleep, so I got up and began writing this.  The state of the world, the absolute idiocy, meanness and short sightedness of politics today, the undeniable enormity of climate change and its inevitable impacts for every organism on the planet, drives me from paralyzing frustration, to near rage, to profound sadness and despair.  Most days all I can do is seek escape and I do this through gardening, reading eclectically, trying to follow some kind of routine, going for walks, a swim or a hike, sharing time with friends or delving into research on plants and the everyday miracles within them and their wondrously choreographed lives here on this planet….I spent my entire morning writing and rewriting this (and returned to it the following day, now today).  It is me ‘sharing’.  Yes, it’s a rant, it’s a bit of analysis, it’s a window into the world as I see it and it contains a hope I have…that I have to cling to most days, for this world and all that lives upon it, because what we have done, what we continue to do, is so profoundly destructive and disheartening to me. Continue reading