Category Archives: What is Life?

“The Ghosts of Evolution: Nonsensical Fruit, Missing Partners and Other Ecological Anachronisms” – A Review and Thoughts on this Life

“The Ghosts of Evolution: Nonsensical Fruit, Missing Partners and Other Ecological Anachronisms”, Connie Barlow, Basic Books, 2000.

The titular ghosts here are the long extinct mega-fauna species that once roamed the continents for millions of years shaping the plant species in question here and, in their interactions, shaped the landscapes themselves. Now absent their animal partners, these plants still retain the characteristic structures that evolved in their long dance together, the genetic inertia contained within their DNA. These plants remain today as anachronisms, seemingly misplaced curiosities with no existing, obvious, reason for ever being, mysteries of form and function, that only begin to make sense when we look far enough back.

I only recently came across this book while doing research into my continuing interest and focus on what exactly is ‘life’ and what is it that distinguishes living organisms from other matter. This book is a little outside of this topic, but not by much. Barlow here is concerned with the process of natural selection and how species have come to acquire and retain their physical and functional characteristics, how they’ve retained them long after the shaping forces have disappeared. While there is a somewhat random element in the process of evolution, organic forms follow patterns and particular patterns are ‘selected’ over time through the ‘working’ of shaping forces. Forms are supported or not,  Once acquired they remain disappearing with a particular species when it is no longer supported enough and goes extinct. This ‘opens’ a niche for possible other species to fill.  Each species is time limited. Each is a process or event that continues so long as it is adequately supported.  It in turn fills roles in the lives of other organisms, other species. Natural selection is not some process relegated to the past, but an active, ongoing, one, though we tend to fail to see it around us. We have a tendency to expand the ‘now’ and attribute to it a precedence and persistence that it doesn’t have and so we also fail to see our own role in the continuing ‘work’ of evolution. We all know something of the concept of the ‘survival of the fittest’, a process that suggests that today’s species are the ‘best’ fit given the conditions in the world today.  Barlow, and the scientists who support this idea, argue instead that today’s species are the best fit for the past as a result of thousands, even millions of years of evolution. Today is just a moment in time. Our imagining of it as something broader and more stable is a problem. Continue reading

On the Chaotic Unreality of the Real and How We Redefine It: Reimagining Reality in a Probable Universe

Jean Auguste Dominique Ingres, The Grand Odalisque. Ingres was a Neo-Classicist, who attempted to create images that mimicked ‘reality’ even as it distorted it for effect, lengthening her spine and her impossible twist of pelvis. Ingres began painting at the beginning of the 1800’s in a world coming to be dominated by Newton’s mechanical view of the universe. Realism would become a dominant style by the end of Ingres’ career. The solidity of reality. What is, is!

Because the pace of change in our scientific understanding of our world, and the technology which follows it, is increasing at greater rates in recent decades than at any other time in our history, it has become ever so more important that we have at least some basic understanding of that science and technology, that we as a society wield in this world…without this, we are literally blundering in the dark, blindly upsetting systems and cycles, upon which our lives depend, with little understanding of our responsibility for the decline or grasp of our own agency in setting the world back to rights.  The advancement of science is an outgrowth of our curiosity as a society.  It is a look behind the ‘curtain’ that too many of us take for granted.  The technologies that spring from these scientific advances carry with them consequences which amplify our individual impacts while providing us with promised advantages through a marketplace that too often only wants to sell and profit from its latest innovation, with little concern for its overall impacts.  As long as our basic world view, our grasp of science, remains stuck in the past, in the more ‘simple’ classical world of its roots, we are more easily swayed by advertisers and pitchmen who’s business demands that we not look too deeply.  We are not, and can never be, ‘experts’ in every field.  The demands and rigors of scientific advancement have a very high bar, but it is essential, especially in these days, that we understand basic concepts, that we have some grasp of how science has redefined the world making possible those technologies which we either wield clumsily, like a weapon of destruction, or more tactfully and respectfully like a surgeon and healer.  As long as science remains esoteric and remote, ourselves ignorant of its ‘message’ and, by extension, ignorant of our own impact on the world, we place all things at risk. 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)

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

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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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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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

The Basic Code of the Universe: The Science of the Invisible in Physics, Medicine and Spirituality – A ‘Discussion of Ideas’

A1SRgFYkq3LThe Basic Code of the Universe: The Science of the Invisible in Physics, Medicine and Spirituality, is not an ‘easy’ read…such should be expected when a book challenges not just our understanding of the world, but even the accuracy of our perceptions of itI  This is leading edge thought in the sciences today coming at a time when the basic precepts of science are being called into question by the political and religious right. The last several decades have seen an accelerating rate of scientific advancement at the same time that the general public’s understanding of it is dropping ever further behind.  Today while advocates press to re-emphasize STEM (Science, Technology, Engineering and Math) in public education, another segment has been working in opposition demanding a return of public education to the ‘3 R’s’, in keeping with the ‘fundamentals’ of Christian conservatism.  This vocal minority rails against our acceptance of a science that questions their ‘world view’ arguing that science’s ‘valueless’ methods poison our ways of thinking raising doubt, putting people in conflict with their basic beliefs and the dogma they espouse.  These people question science’s relevance and wish to look no further than the fundamentalist thought of their religion.  Such doubt and rejection should be raising red flags around the world as people, drawn to their own ‘righteous’ paths, find themselves increasingly in conflict with others on their own separate path. 

I, myself, have always been drawn in many directions, fascinated by one topic then another, but over time forming a rather comprehensive overall interest in the world…more wholistic.  I will never become ‘expert’ in one thing, finding life and our place in the universe endlessly a wonder!  So, I find myself drawn into such topics as evolution, quantum biology and the physics of life, fleshing it out with studies into the particularity of place, places like South Africa, Chile, the Canary Islands and our own Pacific Coast region of North America, with their particular geologies and living communities.  I find the ‘big questions’ the most interesting and will sometimes put considerable energy into trying to understand their possible ‘answers’.  I ‘intuit’ and combine, finding that our world has been so committed to the narrow and fractured views of our countless experts that our understanding of the world and our place in it has become ever more ‘confused’…so again, I am drawn to this and books like this. Continue reading

Death and Life in the Garden: Learning in the Garden Classroom

As gardeners our hands are ‘bloodied’ with the chlorophyll of plants…while it may not stain us as ‘murderers’, we are never the less complicit in their deaths…as much as we are necessary for their lives.  Without us, as a group, these garden plants would never would have been propagated and, if not for our ‘selfish’ acts in the garden, choosing, designing and displaying them, many would be passing into obscurity, most of us knowing nothing of them or of their loss, their passages into decline and extinction, even more quiet, unnoticed, as too many already do today.  While we may acquire and attempt to grow them with the ‘best’ of intention, eventually, they will all die, ill fit or not, suddenly or after many years in our gardens, as a result of our ignorance, impatience, simple curiosity, our desire for something ‘different’, or even in spite of our best informed efforts.  Death comes to all things and our gardens are no exception.  Our gardens art artificial after all, creations of our making and they do not comprise a viable population that will out live us, reproducing in place, making the adjustments that they must over time to survive.  To do this would take an unprecedented amount of effort and coordination on our part and that of our neighbors.  The setting of our gardens are unique to us and their purposes are much narrowed and more intentional than are the places their progenitors come from, the ‘gardens’ of their origination.  For many of these plants our relationship with them might best be thought of as student to teacher as nature sacrifices itself in an attempt to teach us of what is being lost, ever since we stepped out of the loop that once put us in daily direct contact with nature and came to embrace this modern world and its expectations of consumption, ‘ease’ and never ceasing growth…so it is not ‘murder’, it is life, an attempt to return and reclaim.  There is purpose to be found in our gardens, well beyond surface amusement and distraction in what is too often becoming an ever uglier world, or for some of us our need to impress in a game of one-upmanship.  Nature demands more of us, that we accept our role as student and become careful observers, willing acolytes…maybe even crusaders….Too much? no, I don’t think so. Continue reading

Evolution, Speciation and What it Means to the New Phylogeny: A Primer for Gardeners, Part 2

 

 

Understanding the New Phylogeny of Angiosperms, part 2

We tend to think of evolution as a historical process, something that occurred in the past which has resulted in life today, with us at the pinnacle.  Humans with our opposable thumbs, our relatively high ratio of brain to body mass, our consciousness…our souls, we often argue, are the ultimate life form.  We have a hard time imagining that this is not the case, that we as a species, are a part of a continuing process, that some day will fade from the Earth, as other species, more evolved and complex, develop.  This is what happens to organisms over seemingly impossible long periods of time. It has happened and is still happening to plants.   It won’t happen today or tomorrow and this doesn’t mean that what we are or what we do doesn’t matter…because in evolution…’everything’ matters. Continue reading

Life Inside the Cell: Waking Up to the Miracle, part 1

[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.  This first ‘installment’ concerning life within the cell, is divided into two parts, the first covers the function of the cell itself and, importantly, the role of water in the cell.  The second, part 2, 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 of understand and classify 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, 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 of life in effect on our little pieces of ground and the Earth.  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