Bare Bones Biology 319 – In the Beginning

160522-Canyon-asc_4204RLSsSomething like 13.7 billion years ago, give or take a billion or two, so says the dominant theory of our physical sciences. And after the big bang came the creation of many abiotic (nonliving) systems and subsystems until there was our earth, circling our sun, within our solar system and then something like 4.4 billion human years later — here we are.


4.4 billion years of the creation of an earth system that consists of what modern authors refer to as “nested systems” and old-timey basic biological scientists, who didn’t have a clear vision of what is a system – we referred to this as “levels of organization.” And when Darwin and his kind came along, we realized that levels of organization of the Life of Earth reflect most of earth history, written in the language of DNA and RNA, that is (crudely and incompletely put) the Language of Life. Because of the deep nature of systems – their ability to maintain themselves and to communicate with each other, Life of Earth evolved.


It looks like a miracle to me, and our history justifies the concept that is increasingly heard – I think the famous scientist and writer Carl Sagan may have been the first to say that we are the voice, the eyes, the mind of the universe, and because of us, the universe can now perceive itself.


Elegant idea.


And of course it is not false, but it leaves out a lot of other things that are true about the Creation, and it implies – not to Sagan I think, but to many or most moderns who were raised on sociology rather than physical or biological science – it implies that humans are in charge.


160619-canyon-asc_4417RLSsWe are not. What is in charge is that which created the systems, whether we choose to think of it as God or as the Laws of Nature — what we have here is a set of natural laws that were not created by humans, nor are we the first, and certainly not the last word on its eyes, ears or mind. We are less than a pale image of the Creation and the Creator — only one of the millions of systems so created.


But we have indeed magnificently understood the laws of our own creation, and a beautiful story it is.


Let’s just take the nested systems idea. I’m pretty sure people thought about nested images before we had the science to confirm it’s validity in a fact-based sort of way, but I was not here, so let’s begin with a modern view.

First we saw the “levels of organization.” That is now viewed as the levels of complexity of the nested systems. A man is more biologically complex than a kidney. that is more biologically complex than a tissue, that is more biologically complex than a cell, that is more complex than the abiotic systems of which it is composed. Putting them all together to recognize a system which functions to maintain life is certainly an insight worthy of note. And then we went a step further, in the basic science of embryology, and we thought: that looks like an origin story. Ontogony (individual development) recapitulates phylogeny (evolutionary history). And there is reason to believe that our now did indeed evolve out of our yesterdays – the simpler systems that were.

Not very long after that realization, we began to understand that we are not at the top of that pyramid of developmental complexity. Just as our organs, tissues and cells work together to make a living organism (us) so we organisms function together with our environments to make a larger unit of life, the ecosystem, and yet more inclusive is the whole of the Life of Earth, the Biosystem.


I’m leaving out a lot of steps, to make the overview more clear, but even so, in the light of modern mathematical concepts of complex systems and information transfer, the idea of levels of organization seems now, looking back, quite primitive and two-dimensional. And the idea of nested systems also, because if I am a system and you are a system, clearly we are not only nested, but also parallel systems, and that might be why some mathematicians come up with theories that are expressed as multidimensional.


But still, in the beginning, we each arose, one system out of a simpler system out of a yet simpler system, and we each are systems that are nested, or should I say nestled, in the sweet verdant arms of our same environmental system of Life of Earth, which is the other half of us all together.


If we choose to not destroy it.


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Bare Bones Biology 302 – Systems

            “Is our economic system really a natural system? Other interdependent non-linear systems here on Earth are very much life-supportive. But our economic system, based on agriculture and private property, is ultimately anti-life. Therefore, I begin to wonder about its metaphysical status.”


Definition: A “naturally evolved system” can be defined as a group of nodes, connected by links, that function together to maintain the integrity of the whole system. A naturally evolved system is capable of sustaining itself – by means of its emergent properties — within the environment within which it evolved. Generally speaking the nodes are things, objects, that function to connect the links, which are processes or behaviors based in energy and/or information. I’m sure we can improve this definition, but the general idea is that a Naturally Evolved System initiates, evolves and maintains itself within the milieu of other NE systems that compose our Biosystem.


Answer to question, first sentence – Yes, our economic system qualifies as “naturally evolved,” for three reasons. One is by definition another is that I have been watching it grow with that question in my mind, and have become convinced our corposystem is the product of systemic evolution, and not a direct result of human intent. In fact, the corposystem was not the intent, for example, of our constitution, nor, I’m sure of most Americans. The third reason is that our corposystem is using its emergent characteristics to try to sustain itself at a time when its emergent characteristics are not sustainable. The primary function of a NE system is to sustain itself. If our corposystem were directly controlled by human will, it would not use the same methods to sustain itself that are now (in changed circumstances) causing its demise.


A useful metaphor in our effort to “think like a system” is to describe the emergent properties by which that system primarily communicates with other systems in its effort to sustain itself. Systems interact with each other using primarily energy and information. Growth by domination for profit is an emergent characterization of the corposystem, in my opinion, not limited to agriculture and private property to generate growth for profit; it will use any means of domination.

The emergent characteristic of the Biosystem Life on Earth or Life of Earth.


I might argue that the corposystem is based not on agriculture and private property, but on that paragraph in the charter of corporations that requires them to make a profit regardless of consequences. And the same requirement of “nonprofits.”   That little paragraph could very well be the Achilles heel of the corposystem, if we were to take arms against it. However, first questions first, we are talking about systemic failure, so we need first to understand what has failed.


Implication: If we want to find root causes of systemic problems, we must try to understand — not the nodes; not the links; not the designed elements or tools — but the emergent properties and the natural laws of energy and information that affect, create and evolve systems.


Question re sentences 2 and 3: Should we expect nonlinear systems to be life-supportive?


Answer: Certainly not, natural evolution within Life is primarily a process of rejecting systems that are non-life-affirming. We, the corposystem, are being rejected because we are part of a nonviable, naturally evolved system. The vast majority of all naturally evolved systems are rejected outright or become extinct as they threaten the welfare of their own environment (a bigger system) or niche


Implication: Our systemic problems are caused by the fact that we, as a naturally evolved system. are being rejected (becoming extinct). If we want to do something to alleviate this problem, we should be studying how naturally evolved systems evolve.


Question re sentence 4: I think human metaphysics may be irrelevant to nonhuman systems.?? Every system (because of the laws of evolution) must be unique. I think the study of humans and their metaphysic is not the solution to a problem caused by an entity that is not human.


If we save ourselves – then is the time to analyze our behaviors – toward sustainable relationships with our neighboring naturally evolved systems.


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John Scales Avery. 2012. Information Theory and Evolution, 2nd Edition. World Scientific.



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Bare Bones Biology 300 – Responsibility

At the turn of the century, with the help and support of others in my communities, I finalized my scientific “life’s work,” a holistic description of a mammalian system, and preserved the mouse colony so that it would be available for others, and collaborated in the writing and publication of the book.


160219-Mountain-asc_2790s copyAnd then I stepped out into a strange new world, in which people for the most part seem not to like each other, nor to understand naturally evolved holistic systems, including collaborative human relationships aimed toward common goals.


Except for war. Of course that is why we enjoy war. It is our community. Our naturally evolved system, the corposystem, the worldwide corpo-political-social system. A world where people mostly enjoy hating each other and/or fighting and bullying, or fleeing the devastation. Where people believe that we can solve problems by pretending they do not exist or by blaming someone else, or by sacrificing ourselves to individual human goals that are impossible to achieve. 


So I spent about another decade, more or less, studying the genetics or rather the evolution of our human corposystem behaviors, while looking for a role I can play that conceivably might succeed and to help solve our human survival problem. Which of course is real, serious and imminent – and relates to natural law, so it does not respond to human bullying and does not care about our excuses, denial or reasons why we can’t do what is necessary and do-able.


160219-Mountain-asc_2764RLSs copyIt was obvious to me from day one of this century, when I stopped thinking about mice and turned my attention to people, that we humans are behaving, as a group, in a way that makes no sense within our environment, and we cannot survive outside our environment.   And I know WHY.


Because the other half of ourselves – individually, mentally and physically — IS our naturally evolved environmental systems, and we do not care about our environmental systems in the same way that we care about our physiological subsystems.


Even most or many scientists, activists and educators do not understand WHY our corposystem behaviors do not make good survival sense; therefore, for the most part, we all are doing more harm than good, no matter our intentions. We are working for growth, money and dominance, rather than survival. Nearly all of us. At this time in our development, that kind of behavior is counter-productive within the environmental systems of which we are a part.   It is my misfortunate that my life and career rather uniquely prepared me to be one of the knowledge-holders within our current social system, the corposystem.


M'Donna-IMG_20151003_125919151LSsAny knowledge-holder within a social group or species has a responsibility to make her knowledge available to the whole group, whether or not people want to hear about it, so this is my responsibility – it is our responsibility – it is what we must do, if we want to save our species:


1- We must take control over our population growth in some other way than requiring people to be born and then trying to reduce the population – and the problems caused by overpopulation — by killing people off. The killing is not a solution to anyone’s problems. We do have birth control. I know all the excuses; don’t bother to tell me; the universe does not care about excuses. The universe cares about HOW naturally evolved systems function together to survive.  We reduce the population or we die off as a species.


And while we are doing that, we can proceed to develop a human future that is sustainable.


2-   We all, and particularly the world of religion, need to understand how the living earth system was formed by evolution of increasingly complex naturally evolved, interacting systems, and incorporate this knowledge into the religions.


All religions focus on the same light, AS DOES SCIENCE, and it is time to begin acting as though the light is more important than our human wars/debates/dominance behaviors and rituals that do not relate to our current human environment. We can take a lesson from the responsible leadership of His Holiness The Dalai Lama. Not necessarily his Buddhism, but the wisdom of his leadership.


3-   We need to learn how to discuss problems and then discuss them. We ALL need to align our worldviews with factual reality as best we can. That does NOT and should not require either debate or silence. Debate is practice for war, and silence is abdication of our responsibilities to our others. Good outcomes of discussion require good research, good listening, and communal discussion of our current Limiting Factors within our naturally evolved Biosystem Environment. It’s not supposed to be easy, or fun, or happy-face — but it can be rewarding if our genuine goal is survival of our species rather than being better than other people and other species.


4- My personal responsibility is to keep myself healthy and solvent until I can make available a description of how naturally evolved systems function to maintain themselves, and propose one possible recipe for how we can, or could, align our worldviews with the factual reality of natural law by good research and communal discussion.


When this is done — then it will be up to all of you: heads or tails, do we want to grow a future, or just pretend to be happy trashing the future that my parents’ generation tried to give to us?


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Lamoreux et al. 2010. The Colors of Mice: A model Genetic Network. Wiley-Blackwell.

The Dalai Lama. 2010. Toward a True Kinship of Faiths. Doubleday.






For Those of you Interested in Some Positive News About Economics

Anomalous economists to convene at Santa Fe Institute


Reprinted with permission of Santa Fe Institute Update (Follow SFI online at
Last year, at Her Majesty’s Treasury in London, a global team of economists calling themselves Curriculum Openaccess Resources for Economics, or CORE, launched an ambitious, unconventional project.

This February, CORE will meet at Santa Fe Institute to discuss how to make sure their anomalous efforts have a lasting impact on how students learn economics – and the way they think about science.  “CORE is teaching economics as if the last 30 years had happened,” says SFI Professor Samuel Bowles, one of the group’s founders, referring both to the financial crisis of 2008, which took many economists by  surprise, and the growing acknowledgment among economists that not everyone is entirely selfish as traditional economic theory asserts.


CORE’s interactive ebook, The Economy, is not your usual Econ 101 fare. First, it emphasizes identifying and modeling empirical regularities rather than developing mathematical models from a set of abstract, often dubious assumptions about economic behavior. Second, it focuses on fundamental issues that are connected to economics but that other texts tend to ignore – issues like financial instability, wealth creation in capitalist societies, inequality, and environmental sustainability.


Students come to economics wanting to tackle those problems, and recent innovations in economics have a lot to say about them, wrote CORE director and University College London professor Wendy Carlin recently in the Financial Times.


As striking as the book’s content is the price. Competing textbooks sell for upwards of $200, but The Economy is free and available to anyone with an internetconnected device at


“Meeting at SFI is a natural for CORE,” says Bowles. “We are teaching first-year students to think about the economy as a complex, dynamical system and to beware of static metaphors and disciplinary parochialism.”  The question now, Bowles says, is how to ensure that CORE continues to grow and mobilize the diverse inputs from teachers, students, and other users. 

Others contributing to CORE are SFI External Professors Rajiv Sethi and Simon DeDeo. n

Bare Bones Biology 284 – No More War

It may have been best expressed by someone who years ago told me that humans are trapped in a cycle that he claimed cannot be broken. I believe the cycle could be broken, but not so long as we won’t talk about it. So long as we ignore the basic cause of this cycle, we will simply rotate that wheel one more time.

From horror to recoil to compassion to (what, maybe ego or pride or ignorance or all three) that leads us back to horror again.


My fathers’ generation, in their deep commitment to “no more war,” made some mistakes. As a result, I have watched the full cycle in my life, from WWII to WWIII. The greatest horror for me is that we are responsible for WWIII.

I want to talk about those mistakes because we are still making them, and because they are the focus of my activism.


My premise is: if God created the world (and the universe, but my interest is the living world) then the ways in which it functions – that is the Laws of Nature that geCyclenerate and sustain Life – are what they are because God meant them to function that way, or because that is the only way they could function to give rise to what we think of as Life. And finally, my premise is that we are collectively ignoring some of these laws of nature that we DO understand but that we don’t like. What I call the down side. In other words, that we are accepting the part of God’s works that we like and shunning/denying the part we don’t like. The relevance here — we humans do know that Life (including us) operates in the present time as nested and interacting systems governed by natural laws, and not like an either-or pendulum as some earlier humans believed; but we ignore the implications of that fact. If you don’t like God, it changes nothing I have said.

Our western culture teaches us to think in a dualistic, linear manner, like a pendulum or a balance scale, with either-or choices. That world view is useful for making simple machines, but it represents only a small subset of real-world functions of a Life system.


In a dualistic pendulum, the way to prevent wrong is to push back with right and whoever pushes the hardest (or most effectively) wins. This is not how the universe really functions. Our universe consists of nested, interacting systems and their emergent properties. In a system, and we have done a great deal of this in medicine, this is not an abstraction, the way to prevent the illness is NOT to push back at its manifestations, but to cut the cause of the cycle at its roots. The Dalai Lama has said this also.


More realistically, to save ourselves, we must do both. We must push back at the hatred and violence, but that is not enough. If we really want to fix the problem we must also cut the problem at its root cause (rather like cutting the life cycle of a parasite to break the long chain of causes, effects, feedback loops and emergent properties) while at the same time we treat the right/wrong, good/bad symptoms. In our present biological environment, either approach without the other will fail.


If we only cut the root cause without helping the victims who exist today, then millions of people now afflicted will suffer. On the other hand, if we only deal with those currently afflicted, and do not at the same time cut the root cause, then we will have more and more suffering over time. Forever.

What do I propose that we do? How to do it? The first step is simply to stop denying factual realities that t120806-Nukes-ASC_9760hreaten our welfare. Simply discuss the reality, and so replace the denial from which so many people today are profiting on both sides of the love-hate pendulum. Replace it with knowledge about how the system of Life really does function – knowledge and discussion that would of itself expose the profiteers and lead toward solutions.


This is Bare Bones Biology, a production of and KEOS FM 89.1 in Bryan, Texas.


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Bare Bones Biology 274 – Me

Sorry I’m so erratic lately.  Travelling, moving, hot.  And hot under the collar.


Bare Bones Biology 274 – Me



Let’s pretend that humans are not the center of the universe, that we are not omnipotent, not omniscient, and we did not create the idea of systems. Oh, really? Then how did systems get here? Some people claim that our minds generate reality, that it’s all in our heads – that we are the only reality and everything else in the universe is only a human dream.


Good grief! For three reasons.


1) It’s a metaphor, the claim that reality is all in the human perceptions. Metaphors are descriptions of things that are beyond our factual understanding. Most of everything is beyond our factual comprehension.

But the great evolution of basic science is the understanding that factual reality is more powerful than opinions, fantasies and metaphors, that the facts are the rules, and if we don’t follow the rules we die.

150917-Denny'sCloud-ASC_9631RLSs copy

2) Nevertheless, humans are still willing to kill other humans for believing in measurable facts, and a big part of why we do this is because we want to believe in a melodrama that puts us at the center of the system. We laugh at historic atrocities, such as the debate over whether or not the sun revolves the earth, and then we carelessly cause the deaths of other humans, by starvation, war, and a host of so-called “environmental diseases” that are not caused by the environment, but by our own septic wastes, and our overpopulation, that we could control – but we would rather pretend that we are at the center of reality.


In the beginning was the question, and the question was human, but if the question was human – then of course it could not have been in the beginning, because we have answered that question – the physicists have, and so have all of our origin stories, and it is clear that humans were not present in the beginning.


Therefore, humans did not invent systems; there were systems before there were humans. In fact – humans are systems, and we may as well call us evolved systems because everything from the beginning onward seems to have been created by a relationship between the laws of nature and the same processes that subsequently generated LIFE. Like, the first a “big bang,” whatever that was, created matter out of energy, and from that time forward there were processes that obeyed the laws of nature – like, gravity, positive and negative energy relationships, things orbiting around other things, and something I have not heard anyone discuss that causes systems, once they are formed, to maintain themselves for as long as possible.


This is true. The function of an evolved system is to maintain itself, and it has been true from the beginning, so it has nothing to do with whatever economists or other business persons have finally figured out. We knew this before there were economists or physicists or business persons. We just didn’t have a name for it. We called it God or nature or “the forest” or whatever words we had, if any, at whatever time we happened to notice that our environment and the processes that make it operate, are more powerful than we are, and there are rules, and if you break the rules you die.


3) It’s as true as it can be: Humans are not the center of the universe, so all of you who can’t believe that the truth is true – carry on with the barbarism caused by your fairy tales, but at least you should let the rest of us try to figure out something a little more humane that we can do to actually make life better for others, and not only for our own central selves.


After all, we do still have the same choice we always have had. We can face reality and survive, or we can play those silly “me” games and destroy the future of our own species.


This is Bare Bones Biology, a production of and KEOS, 89.1 FM, in Bryan, TX.


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Bare Bones Biology 268 – Systems

I capitalize Life to represent the emergent property of the Biosystem. And life is used represent individual living things.

 The green bits were edited out of the podcast because of time restraints.


How to say it, that’s the problem, and in five minutes or less, it’s difficult. So today I will need to strain my brain and yours, because I want to talk about systems – real natural systems. I will reference a “A Systems View of Life,” co-written by one of the speakers at a previous Bioneers, that I have not yet read, and a book entitled “Linked” that I have listened to about 5 times and benefited every time.


A naturally evolving/evolved system is a set of objects /nodes/things linked together in all or nearly all dimensions by processes or other manifestations of energy. The nodes and links of an  evolved system work together to generate a unitary emergent property (properties/characteristics/phenotypes) that is/are useful to the environment within which the  system evolved/evolves by natural selection.

Implications of this definition follow:


  1. 1. Every kind of system has unique characteristics (emergent properties) that were of value to the environment within which the system evolved. For example, you are a system that consists of subsystems, your emergent properties are Homo sapien. You are a subsystem of our current social system, the corposystem, that is a subsystem of the Biosystem. The defining emergent properties of the corposystem are growth by domination for profit. The corposystem is a subset of the Biosystem, whose defining emergent property is Life.


  1. Every kind of system is unique because its unique emergent properties permit the system to fill or define a new and useful niche within the environment of its origin. If there were no unique niche available that contributes to the welfare of the parent system, then there would not be that subsystem. For example, your kidneys evolved as a subsystem of you because they are necessary for your survival. Your brain also.
  1. In this modern world we need to use that brain – all of it — both the logical, critical faculties and the emotional, instinctual understandings — if we are to survive. That’s what it’s for.

For example, if we reject basic science in favor of humanities – or if we reject humanities in favor of basic science (which is NOT engineering), then we are not using all of our brain power in the effort to survive within the Biosystem.

  1. Each system interacts with its environment through its emergent characteristics.   The emergent characteristics of our corposystem as it has evolved, no longer align with or enhance the welfare of the Biosystem. This means the corposystem is in competition with the Biosystem. Competition is not the natural order of success. Competition leads to extinction of one or other of the partners. Success in the Biosystem requires balance among the parts (think again of your kidney).

Because the corposystem and the Biosystem are not aligned, and in fact are in competition, therefore they cannot both survive unless we decide to use our brain to force a change in the emergent properties (the behaviors) of the corposystem.

5 – The function of a system is to perpetuate itself. If it can’t do this, it will die. One implication of this reality is — if you have been raised within the corposystem — then you have been trained to behave in ways that benefit the corposystem, and our evolved human social system will induce or force you, in many and subtle ways, to behave in ways that promote growth by domination for money.

 For example, one of the ways the corposystem exerts this pressure is to start an argument over some issue of great importance, and then refuse to pemit us to discuss it because it is “controversial.” Especially if it is NOT controversial but factual, the corposystem is afraid of it. If we don’t discuss it, then we cannot align it with the needs of the Biosystem, and our behaviors will support the corposystem world view rather than sustain the Biosystem. It would be like the kidney competing with the rest of your body.

 Ocamora-ASC_8563RLSsTake climate change for example. There is no doubt about climate change. It’s a fact. The only doubt is what we will do about it. To defend itself from this fact (that would require the corposystem to shrink rather than grow), the corposystem first created a fake controversy. But facts always trump propaganda in the long run, and now the corposystem has been forced to take that issue seriously. So the new corposystem propaganda seems to be revolving around schemes intended to make money by promoting climate-change-related growth of businesses and charitable organizations.   The corposystem is based in growth. The growth of the corposystem destroys the Biosystem as we know it.

The Biosystem is changing in effort to maintain its viable balance, and as a result the productivity of the Biosystem is falling and will continue to fall, no matter what we do. Unless we can stop corposystem growth. That is how the Biosystem stays balanced. It is now out of balance and changing to a different climatic form. That’s how the Biosystem gets rid of problem subsystems.

My goal is to help grow a NEW human social SYSTEM to replace the corposystem. The emergent properties of the new system must be sustainability and resilience (at least). This can only be accomplished if we align our behaviors (not our emotions or our beliefs, but our behaviors) with the needs of the Biosystem.

And that is what basic science (not technology) is for. As for systems, our understanding of systems will not save us any more than our understanding of gravity or thermodynamics can save us, nor can technology within the corposystem, because technology serves the emergent characteristics of whatever system is using it.

Systems is just another fact of Life. It can help us align our behaviors – that’s what basic science (not technology) is for.

The corposystem will die in any case, because it is dedicated to overcome the Biosystem using domination and growth. The questions now are: 1) Will the corposystem damage our Biosystem to the extent humans cannot survive in it? And 2) Will we be able to step outside the corposystem world view and grow a new human social system that is sustainable?


This is Bare Bones Biology, a production of and KEOS radio, 89.1 FM in Bryan, Texas.


A copy of this podcast can be downloaded at:



The Systems View of Life, by Fritjof Capra and Peter Luigi Luisi, Cambridge University Press. 2014.

Linked by Albert-László Barabási. Perseus, Cambridge, MA, 2002