Author Archives: gardenriots

About gardenriots

I'm a horticulturist with 35 years experience primarily in the maintenance and management of public landscapes and gardens, including, renovation, construction, planting design, doing horticultural reviews of capital projects and creating and implementing maintenance plans that recognize the dynamic nature of these places. I have a strong interest in sustainable/ xeric landscapes and view the landscape as an opportunity to create places of beauty in an all too often utilitarian urban world while at the same time using them as a teaching tool for the public and peers. I recently retired from Portland Parks and Recreation where I was responsible for many of our downtown landscapes for 16 years. I have a degree in ornamental horticulture and a life long interest in science, beginning when I was ten or eleven with astronomy. I became fascinated by physics and the paradoxes and conundrums theory left us with in the '60's. I moved on from this to an avid interest in nature, biology and the living world around me in Central Oregon. I did not find a mentor so instead spent many hours by myself exploring and wondering and became largely self-taught, a pattern that has continued through my adulthood. Some of my postings are a direct result of my curiosity and are a result of my learning style, submersing myself in a topic that interests me, generally related to a plant I have grown and then building a fuller understanding of what is going on. Topics as diverse as general evolution to quantum biology and learning the biogeography of regions from which my plants come are continuously fascinating to me. These interests can become consuming 'rabbit holes' for me taking me places my wife does not understand. The world to me is a beautiful, fascinating place filled with puzzles to be understood and thereby more fully appreciated.

Song of the Cell: An Exploration of Medicine and the New Human, A Review

The cell is the basic, irreducible, unit of life. Whether an organism is animal, plant, fungal or bacterial, the cell is its basic unit. While it can be broken down into its ‘parts’ for examination, none of those parts are capable of independent life, none are able to continue fulfilling their functions on their own. The cell and its ‘community of parts’ operate as a ‘social’ unit, as a whole. Each ‘part’ fulfills one or more roles in the ongoing life of the cell. This book is a review of cell biology, of the development of our, human, understanding of the life of the cell and its centrality to our understandings of what it is be alive, how it has and continues to transform our practice of medicine. The author, Siddhartha Mukherjee, is a doctor and researcher who has spent his professional life studying blood and its cancers, trying to understand and treat disease. Continue reading

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Fen, Bog and Swamp: A Short History of Peatland Destruction and Its Role in the Climate Crisis , a Review

For another review: link

Novelist Annie Proulx, begins her book with her childhood, giving us an idea of who she is, her attachments to the living world. She takes us with her on a walk she took with her mother as a young girl, through the neighborhood wilds, to an ignored patch of swampland. Her mother loved such places. She places her story in the larger story of the times of her birth and coming of age, of the 1930’s and the cruelties we perpetrated on each other and our limited view of the natural world, a world set as a table before us, for our consumption. She writes of her attachments to these abused and devalued wet landscapes, their necessity for a healthy natural world and what their loss means. Earlier, I reviewed Edward Struzik’s book “Swamplands”. Struzik has spent years working with researchers and conservationists in the field, and writing of his experiences. Proulx’s approach is much more personal as she works to place bogs, fens and swamps into a human, historical and cultural context. Continue reading

Swamplands: Tundra Beavers, Quaking Bogs and the Improbable World of Peat, a Review

The idea of individuality and control, key elements of the American psyche, are a self-deception. We can take an individual action, guided by an intention, and see its effect in the world around us, but after that, the first ‘tier’ of effects, there are secondary, tertiary and others beyond them, as what we have effected spreads out across space and time, effecting those things, beyond our focus, that nevertheless are in relationship, and do and must respond. If we’re paying attention we can see them and attribute them to others, unaware of our impact. The world is so large and complex, while we individually, commonly see ourselves as relatively ineffectual. We often don’t recognize our own agency and how collective effects propagate from our action. This can also support the idea we ‘can’t’, in a significant way, damage the systems and cycles that support life on Earth. What we must understand though is, that as members of societies and cultures, which share economies and technologies, our ‘individual’ actions are ‘shared’, they are multiplied, often many millions of times. We act individually, but we have tremendous collective impacts. By denying this we deny individual responsibility, which in effect, is a cultural denial, permitting the negative impacts to continue. “It’s just me!” “It doesn’t matter.” “It’s their responsibility, not mine!” These collective problems are then left unaddressed.

It is easy to believe this way. There is so much beyond our own control, so many problems, that it must be this way right? No. We are responsible, collectively. We never truly act independently, because we live in relationship with those around us and their, and our, influence over one another blur. Like it or not, we are a part of a larger society. To go against the conventions and norms of society, to act independently, is risky, to ourselves and the world around us…a risk which can bring with it changes, either positive or destructive. However, going ‘along with’ the norms and conventions of society, unquestioningly, is to possibly continue a potentially destructive practice. We are responsible. We have necessary roles o play. We have been relatively bad as a society at discussing our wider actions, of working to understand our impacts and insuring the security of life and its necessary conditions. Too often we comply, go along and continue doing those things simply because we ‘always’ have, forgetting that as our numbers and use continues to grow, so does the potency of our impact. We have been habitually confusing short term gain and comfort, with longer term survival and good. The consequent results of those unexamined actions can become devastating. To continue ignoring our negative impacts on others, in its broadest sense, is ultimately a threat to our own well being and security. Uninformed actions, actions taken selfishly at other’s expense, threaten the whole, because of the ubiquitous and pervasive connections to the world and between all people, places and organisms. Our denials will not change this. So, why do I bring this up? This is a gardening/horticultural post…because, what we do, or don’t do, in our gardens and across our shared landscapes, has impacts well beyond their borders. Continue reading

Spillover: Animal Infections and the Next Human Pandemic, David Quammen, WW Norton & Co.,2012; a Review

If you were perusing the library shelves and came across this book, the title “Spillover” may leave you a little uncertain in terms of its topic, without reading the subtitle and having some understanding of the processes described in the book, the emergence, evolution and ecology of ‘new’ diseases, human diseases. When we speak of them we understand them as conditions, assaults on our health and human bodies, which result in an array of symptoms, with wide ranging severity, ranging from mild and asymptomatic; to bothersome with knowable, short lived cycles; through chronic and debilitating; to those entailing a series of feverish cycles we simply must endure; to those often painful and fatal which wreck havoc on our systems and organs. Quammen, the author, is as always, an intelligent and thorough researcher able to interpret complex topics for the layman while staying true to the science and the people whose stories he tells as he weaves together the larger narrative. Continue reading

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)

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

Democracy, Inclusion and Full Citizenship as Biological Imperative: Arundhati Roy and the Politics of the World

When we open ourselves up to the world, travel to other regions and countries, see and live in different geographies, experience other cultures, climates and biomes, we have the opportunity to be intimate with and understand world’s very different than our own. The world is vast and its peoples and organisms, though astoundingly diverse, are closely related. Even if we could travel ‘everywhere’, having a meaningful experience with all of it is simply not possible. It is dangerously presumptuous to assume that anyone of us might understand all of this. Such travel, should we want to, isn’t possible for the large majority of us, which does not mean that there is therefore no point in traveling to where we can. If our goal is deeper than simply ticking off places and experiences, if we are seeking to understand, to ‘grow’ ourselves, our limited travels can still serve us. For the rest of us it is through reading and the sharing of stories that we can gain such insight, as long as the authors, our guides, are themselves astute observers who are engaged in the places and peoples of which they write. There are many such writers…I can think of none better than Arundhati Roy who writes so beautifully, imaginatively and painfully of her beloved home India. Continue reading

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

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. 

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

Musings on This Life After My Brother’s Death

My siblings and I were all born in Salinas, California. Our dad drove back and forth to the PG&E power plant at Moss Landing on the coast where he worked. He wanted out of California and anywhere north seemed better, so in 1961 we moved to Redmond, OR. My oldest brother was 12, my youngest sister 2 when our family arrived in Central Oregon. We all graduated from Redmond High School before moving on with our lives. My youngest sister, stayed, brother number two, also. The rest of us dispersed.

My brother Kirk had an artist’s sensibilities and talents. For reasons at the time confusing to most of us, he enlisted in the Marine Corps, the Viet Nam war ongoing though winding down. I always thought that this was an attempt to mold himself into something else. He never saw action. I think most of us at the time thought this was fortunate. When he got out he moved to Portland and got involved in his church. This relationship became central to much of his life. It wasn’t something we could discuss. We had been raised in the more ‘flexible’ world of the Presbyterian Church. This was very different. I would characterize his beliefs as ‘fundamentalist’ and evangelical, those who didn’t believe as they did, were doomed, including myself and the rest of the family. It mattered not that others might claim a belief in the same christian god and had taken Jesus into their hearts, as he explained it to me…others were not on the righteous path…apparently it was singular. Not only would those of other faiths, but those christians of other denominations had been ‘mislead’ as well and would ‘pay’ for their error in the after-life. Continue reading

Climate, Trends and Current Weather: A Nice Record Setting Fall Day

Looking south, upstream along the Willamette, to the Ross Island Bridge and the South Waterfront buildings hugging the western bank which house the pool in which I swim..

I puttered and pruned in the garden today until I produced enough waste to fill my yard debris wheelie bin, it didn’t take long. After lounging around and reading for awhile I walked the 2 and 3/4 miles to the pool at OHSU where I swam for 40 minutes, then spent another 1/2 hour doing yoga and some core exercises in my efforts to slow down my inevitable decline…then, I walked back home across the river. It was a bizarrely warm afternoon, and early evening, and I covered the distance in a tee shirt…and pants and shoes of course. Lots of walkers out crossing the Tilikum Bridge and walking along the river. People were taking advantage and enjoying the day. I wonder how many understand just how ‘weird’ this weather is? Continue reading