Category Archives: Plant Metabolism & Photosynthesis

The Way of the Cell: Molecules, Organisms and the Order of Life – A Review (Read This Book if any of the Life Sciences are of even remote interest to you)

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I’m an integrator, a contextual learner and a big picture kind of guy. I am willing to ‘slog’ through the details, the analyses of experts, to understand what is going on, when the details help me understand, in this case, the operation or ‘life’ of the whole organism. What are the processes, how do they influence one another and how does that result in the condition we recognize as the dynamic, animated phenomenon of living. Franklin Harold, a professor emeritus in biochemistry at Colorado State University when he wrote, “The Way of the Cell: Molecules, Organisms and the Order of Life”, in 2003, has produced the ‘best’, and most comprehensible, review I’ve found of the life in the cell, to date. This book does not require an advanced degree to follow. It requires an interest in biology. A botanist, horticulturist or even avid gardener pursuing a more thorough understanding of what life is and what is occurring within the plants and animals around will find much that is accessible to them here. This book is not a slog. It is readable and readily comprehensible, though for those with less of a science background, a little more challenging, but hey, nothing ventured, nothing gained. The jargon he uses I would say is necessary. Science can be very precise in how it views its subject, necessarily so, because meaning becomes lost when the precision of language is too generalized. I’m adding it to my own library. I include some extensive quotes here to give you a sense of his style and philosophy. I also gleaned much from these particular passages. In school I endured too many professors and lecturers who seemed more interested in impressing their students with their own brilliance, and our inferiority, and came to relish those who were true teachers, who were able to impart to their students, there own love and fascination with their topic. Harold is one of these. He set out to write a book that would reach out to the reader making his topic more accessible, more comprehensible and thus widen the circle of understanding…and he has succeeded.

The cell, scientists would agree, is the smallest fully functional unit of an organism, any organism. It is the basic structural unit that has been joined together to create larger, more complex organisms. If you attempt to reduce it any further, divide it into its component parts, which science typically does in its process of reduction to understand it in its parts, it loses functionality and dies. Single celled organisms, bacteria, archae, and the larger single celled eukaryotic organisms, like amoebas, comprise the majority of living species on earth, by both number of species and by sheer mass. They are as complete as any single organism, like ourselves, a Redwood or Blue Whale, can be. Whether a single celled organism or a massive multi celled organism made up of several billions of many thousand ‘types’ of different specialized cells, almost all cells are capable of all of their essential functions, as long as they are supplied with proper nutrients and flows of energy. Cells, as Harold describes them, are highly coordinated ‘societies’ comprised of many millions of individual proteins, enzymes, lipids and ions, with various forms of RNA, bound within a protective, limiting and self-regulating membrane, often with other internal membranes, which protect and allow other more specialized functions within the cell…and DNA, or in the cases of some bacteria, RNA, which contain the ‘code’ which prescribes the organism. It is within the cell membrane where the particular mixes of their constituent parts are held in dynamic flux, where the ‘work’ of living occurs. Within what was once described as a ‘soup’ of chemicals, suspended within a virtual sea of water, the cell conducts the ‘business’ of life. Today we understand that within a single cell water molecules far out number any other substance. Cells possess a complex internal structure, a cytoskeleton, grown from proteins, that is integral to the transport of metabolites, the regulation of its thousands of internal processes, the structure of the cell itself and essential to its ability to respond and move. The actions within the cell are largely self-regulating, influenced, certainly, by outside, and internal energy gradients. The various reactions influence the rate of other reactions in a complex system of feedback loops, with a ‘logic’ often compared to that utilized by a computer. Processes are chemical, electrical and ‘mechanical’ as one reaction induces a conformational change, a change in ‘shape’, of a particular protein or enzyme, which directly influences what it can do. These changes in ‘shape’ act as effective ‘switches’ within the cell, switches operating amongst thousands of other such switches, creating an intricate system of feedback loops which regulate just what the next step will be. Only functions tend not to be linear. They can be extremely complex, with a redundancy that also allows the cell to vary internally widely, while maintaining itself, overall, in a relatively stable state. Its internal complexity then accounts for its responsiveness and adaptability. It imparts a degree of flexibility, of adaptability to a system within the cell. All of this going on at a molecular level that plays out, with powerful effect, at the organismic level. Continue reading →

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Every Life is on Fire: How Thermodynamics Explains the Origins of Living Things–A Review…and a Deeper Look Into the ‘Fire’ of Life..

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This is a book about ‘life’, that which animates particular organic structures, organisms, absent from other ‘structures’ which remain fixed, but for the physical and chemical forces which wear them down. From our human perspective, this sets ourselves, and all other living things, apart from the inert, nonliving, matter that comprises our world and the universe. England, as a physicist, sees the world of nature and all matter within it, differently than most of us. Science has demonstrated that the universe tends to operates under consistent ‘laws’. Organisms, while a special ‘class’ of matter, are still of matter composed of the same atoms joined together in complex macromolecules not found outside of organisms, which are in fact created within organisms. They occupy a different section along a continuum defined by energy, a ‘family’ of complex, shared organic structures. This complexity of structure goes to determining their functionality. Function increases and diversifies as complexity increases, capacities are expanded and the flow of energy through them becomes an effective and sustaining agent in their ‘being’ and evolution. His view is consistent with the many other physicists who have looked into life and view it as an inevitable outcome of the processes, energies and materials that comprise Earth’s particular corner of the universe. Earth appears to be a relatively rare occurrence, but it is extremely doubtful that it is a singular one. Given the particular mix of ‘ingredients’ and energies here, matter has come together over the course of over 4 billion years to form life as we know it because it could and whatever is possible/probable tends to happen with a degree of frequency. Particular patterns precede those to follow, not necessarily determining them, but increasing the likelihood that they will. The flow of energy through matter tends to ‘favor’ a range of outcomes. Those outcomes tend to favor the next, building from one ‘success’ to the next.

Many of these patterns and energy flows occur at molecular levels well below our ability to observe and measure. These patterns are not generally obvious to us.  Our perceptions are shaped by our beliefs about the world. We tend to ‘see’ what we expect to see, not necessarily what is there. We shape our perceived world into the commonly shared story that has been passed on to us. Our particular indoctrination, our educations, all go toward determining what we see, then we take our experience and use it to reinforce that understanding. In a sense we ‘choose’ our reality. From the moment we each open our mouths or put word to page, we do this. Our language and knowledge limit us. It requires that we distill our perceptions, our experiences and our understanding into a comprehensible form. We are then limited by our biases, our language, what we already ‘know’. We are all at a ‘remove’ in this sense, apart from the world in which we live, although we are intimately immersed in it. As ‘western’ people we tend to see ourselves as separate from it. In actuality, we can never be so. England looks into this question of what life is by taking our modern and still developing idea of ‘thermodynamics’, our study of energy and the way that it ‘works’ on the stuff of the universe, on matter, as his way into this ‘story’. Energy is transformative. Matter, is arguably, a particular expression of energy. One can be translated into the other.

England is a theoretical physicist. You will not find in this book a detailed explanation of the living organism or even a detailed description of the flow of energy through one. Thermodynamics and his idea of dissipative adaptation are larger concepts that can give us a framework for understanding the bigger picture of an almost unfathomably complex topic. England joins with those today who would argue that any living organism is not so much a thing as it is a process, in a state of continuous change, a process which both follows a probable, understandable, path, and is itself a part of the larger/longer process of evolution, of becoming, building on itself and life’s many patterns, as it moves ahead through time toward something unknowable to us. We exist from moment to moment, a ‘response’, one of a particular and massive set of more or less likely probabilities, each which influences what will follow, within a universe of definable ‘law’. Here England gives us an intellectual framework for understanding the processes at play in this process of living. Living organisms are conductors of a continuous flow of energy through them from outside and back after it has degraded. This flow of energy acts in very particular ways on the molecules, cells, tissues and organs of an organism…until it no longer can. An organism, is in a sense, a conductor, a channel through which energy flows from a higher, more available state, to a lower, less available state. Energy drives them, permits them and enables them so that they are in this sense ‘self’ sustaining…as long as the energy flows and the organism can maintain the integrity of its structure at all levels.

The following is an extensive quote from his book: Every Life is on Fire: How Thermodynamics Explains the Origins of Living Organisms, pp. 113-116.

“…a plant—for example—has to be thought of as holding steady on a steep [energy] hillside in a constant state of free fall. Much like the chemicals in a battery powering a flashlight, many molecules in a plant are constantly undergoing reactions that convert them into other, lower-energy forms. At the same time, randomizing thermal fluctuations are taking the specially ordered components of each cell that have been assembled in a particular fashion and wreaking havoc with them, either through chemical damage or via larger-scale physical rearrangements. In permanent darkness, a plant is therefore on a slow road to death, for dying in physical terms is nothing more than sliding downhill in a variety of chemical and physical ways. Of course, plants can survive just fine for a while in the dark, but not forever. [Animals, for the most part exist in a much more precarious balance requiring much higher energy flows for a given mass.] Eventually, the twin tendencies to lower energy and higher disorder that are required by the fall to thermal equilibrium will win out, and the pile of matter that was originally a live organism will start to look less and less like one.
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A Review and thoughts on Peter Hoffmann’s book, “Life’s Ratchet: How Molecular Machines Extract Order from  Chaos”, Basic Books, 2012. 

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This is a relatively technical book, one whose title, with its definite mechanistic spin, nearly stopped me from reading it. In this Hoffmann begins with a history of science and how we have looked at life as a remarkable process from the days of Aristotle to today and how that has shaped our inquiry and our capacity to understand it. Is life possible only because of some inexplicable, and yet unknown, ‘vital’ force? Are organisms endowed with this gift of life by a creator? or are there physical laws which shape and determine life? There has been a long ‘battle’ waged between the various ‘vitalists’ and mechanists, the later who once viewed an organism as a special machine, popularly comparable to a watch or clock, animated by a ‘vital’ force, who over time evolved their search into that of more recent times of seemingly fantastical molecular mechanisms, ‘engines’, within an organism which, because of their nano-scale can perform and behave in ways that appear incredible to the layperson. Continue reading →

“Entangled Life: How Fungi Make our Worlds, Change our Minds & Shape our Futures”: A Review

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Sheldrake, Melvin, “Entangled Life: How Fungi Make our Worlds, Change our Minds & Shape our Futures”, Random House, 2020.

I have spent most of my life outside amongst, growing, observing or studying plants and yet, every page here has caused me to take at least a moment to reconsider the life I’ve been so involved with. Everything here underscores what I’ve read and learned elsewhere, sometimes casting it in an entirely different ‘light’. While we learn to think of organisms as discrete individuals, fungi, a class of organism separate from the bacteria, plants, animals, even viruses which I’ve been examining, are impossible to consider on their own without looking into their vital relationships with the other forms of life.  While all organisms depend in many ways, great and small, upon other organisms for their support and sustenance, fungi are nearly impossible to imagine separately, their ‘bodies’ being literally intertwined in and around those of others.

Relatively early in the book, Sheldrake describes the difference between fungi and animals in this way, animals put food into their own bodies, fungi put their bodies in their food, digesting what they require by secreting acids and then drawing the broken down nutrients back into their mycelial bodies and transporting them to where needed. Continue reading →

On Life: An Annotated Reading List of Titles Exploring the Physics, Biology, Evolution, Natural Selection and the Generative Power of Far Out of Equilibrium Dissipative Structures (Organisms)

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Nurse, Paul, “What is Life?: Five Great Ideas in Biology”, WW Norton and Co., 2021. I’m placing this book out of order here, its American edition just released this year and I’ve only just read it, because I concur that this is an excellent introduction to its topic and should be accessible to a broad audience, one without an academic background in biology. It does what Carlo Rovelli’s “Seven Brief Lessons on Physics”, does for its readers, presents in a compact and cogent way the central ideas for understanding the science of life. Nurse, is a Nobel Prize winning geneticist and cell biologist, who has dedicated his research life to the study of the cell and what sets this class of matter apart and unique, looking into its structure, chemistry/metabolism, reproduction, evolution and the relationships and communication which must occur within and between cells. He looks into what genetics is and isn’t capable of, what it seems to control, the genes for 20,000 some different proteins included within our DNA, while leaving open to question the instructions and detailed directions, how the growth and development of an organism is actually determined.

The reader will benefit from having some basic understanding of chemistry to fully grasp what he writes here, but this is an excellent starting point.  At 143 pages this book shouldn’t scare off the reader.  This is a window into life and should peek the readers interest as Nurse reveals what he still finds so fascinating about life and this world.

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 redefining 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 may be 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 so 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

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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

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It does snow, but usually no more than a couple very wet inches at a time. This is mid-January ’17, by some measures our fifth most severe winter in recorded times.
Monte, in mid-June of ’19 prior to any sign of flowering.
Agave montana with a friend’s Mini- taken last year, Sept. ’18
The site is exposed fully to the south and slopes to the west at about 5%. Oct. 10.

 

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

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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

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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

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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 →