Category Archives: Growth and Cell Division

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

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

Physics, Evolution, Natural Selection and the Generative Power of the of Far Out of Equilibrium Dissipative Structures (Organisms), part 2

Chemists have often argued that everything is chemistry and if you don’t know about it, what can you really know of the world? A current Periodic Table, one with considerably more elements than were contained in the table from my high school chemistry days, this one including many of those transient elements created in particle accelerators. These ‘new’ elements are very unstable and breakdown rapidly. Some are thought to have existed only at the beginnings of the universe…sometimes in its first moments or during vanishingly rare exceptions. I know, this is very ‘nerdy’, but I go to the interactive table on the linked site frequently to learn about the particularities of elements of interest to me. That table responds to your questions about changing ambient conditions and their physical ‘behaviors’ and capacities for particular reactions. Check it out.

On Pattern, Chemistry and Life

Pattern builds upon pattern.  Whatever you start with effects and limits everything that follows whether we are talking about masonry bricks and stone or Eukaryotic cells and organic molecules.  A different starting point or ‘decision’ at any point in the process, effects every ‘decision’, or even possibility, there after, effects the likelihood of what is to follow, shapes the possibilities, the future, through the evolutionary process…but does not determine it.  To speculate whether other amino acid groups are theoretically possible does nothing to change the course we are on.  The capacities and characteristics of your most basic components set the stage for all that follows, the brick analogy only takes you so far.  Bricks, no matter what you do with them, are very limited in what they can create…how they will ‘behave’ when structured as a wall.  They do not, when combined into a structure, acquire properties that no single brick had before their assembly…their futures were ‘decided’ the moment they were made into bricks.  They remain bricks. 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….

Continue reading

The Flowering of Monte: Going ‘Viral’ During a Pandemic

 

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

COVID-19, Pandemics and How They Will Change the World For the Better

I’m not a biological ‘fatalist’, but there are several reasons why epidemiologists were attempting to plan for a pandemic and why the Obama administration was empowering institutions, creating protocols and organizing resources that could be mobilized quickly, before the COViD-19 outbreak, not for this one specifically, but one of some kind. Viruses, bacteria, mycoplasma and other microbes fill the world at a microscopic level…they are everywhere, all of the time. Our own bodies contain far more of them than we do of our own some three trillion cells. Fortunately, most of them do not cause us disease, at least as long as we remain healthy. Many of them, in fact perform valuable functions in us, beneficial ones, without which our lives would be the poorer. Disease too is part of life’s ‘plan’. Its agents are dynamic. Today’s diseases are not those of the past. We evolved together. They mutate and sometimes ‘leap’ across species boundaries. A study of biology and disease reveals a function of disease or at least a consequence to the health and evolution of a species. It may sound heartless to put it this way, but disease is very much a part of living. With this new disease, COVID-19, as with others, it is selective, affecting those whose health is compromised in some way disproportionately, killing those most susceptible, the weak and those may include those surprising to us. As in most things concerning life, nothing is so simple as our concept of strong and weak. Disease is a part of the process of natural selection that has always been in effect in the world. Continue reading

Viruses in Plants: Life, Disease and Evolution

Gardening for most of us is more than just a distraction, but these days, in light of the coronavirus, SARS-CoV-2, the disease it causes, COVID-19, the conflicted messaging we’re getting from our ‘leaders’ and the insecurity many or most of us are feeling around our own financial situations, we are likely more in need of one than we had been. This post will be a bit of that, while at the same time an attempt to shed a little light on the issue of viruses in the plant world. Yes, viruses plague plants as well, but they are also thought, by more than a few scientists, to have played other roles as well, such as in evolution, a process that continues to and beyond this day! In some ways they parallel those of bacteria. Both viruses and bacteria can cause disease. The disease that a virus can cause is generally very limited to a narrow range of species, even to one, with notable exceptions. Most, however, perform other tasks as they go about their ‘business’, within the bodies of bacteria and larger multi-celled organisms. In fact most viruses, like bacteria, play no direct roll in our health…and they are everywhere.

It is important to understand that science has its own biases and that our perspective as mortal human beings affects how we view things as well…viruses included. Science builds on experience. It requires that new science, and its theories, be consistent with what is ‘known’, but it must also be open enough to avail itself to new understandings when it better explains previously accepted theories. What do I mean? Viruses ‘cause’ disease, but might they also be something else? If our biases set us up to see them agents of disease, reservoirs for future disease or inconsequential, we will fail to see what they may also be…and there are some who would assign a much more important role to viruses and see them not just as disease agents, but as far more, as essential ‘elements’ and players to life today and the processes that made today’s form of it even possible! First, though, what do we ‘know’ of viruses. Continue reading