Bare Bones Biology 307 – I Didn’t Do That

Yesterday was not good for me. First I had two doctors’ appointments; second, they were both 100 miles away; third, I drove from my mountaintop to theirs and back, all in one day, stopping for medication on the way back, and then zonked out under my electric blanket by 6 pm. Just before midnight I woke up, went out to my little travel-trailer workshop, turned on the electric space heater, and all the lights went out in our entire subdivision.

I didn’t do that.
160320-SantaFe-asc_3694RLsDid I?

So, using battery power, I checked my emails, which consisted of about 50 political flyers, one of which I read because it did not have any fantastical, tremendous, horrendous, unbelievable, hyperflagulous words in the title.

While I do not write about politics, I do write about how systems function, and these words from Bernie Sanders could have been me – talking about naturally evolved systems that have nothing to do with politics.: “. . . the American people understand that you cannot change a corrupt political system by taking its money.”

And this is my version of essentially the same reality: “When I say that we may not succeed in implementing your mission, I am not referring to what you can do today to help other people who are caught in the system – what I mean is that what you can do today will not accomplish your long-term heart’s desire and frustration, which I believe is to move up one level of systemic organization — from helping individuals, to changing the system that creates these victims — and in fact what you do today could, unawares, enable the system’s creation of victims. “ Bernie said it better, but that’s the way I talk.

About two hours later, the lights came back on and I went out to the little workspace and turned the heater on again. Nothing bad happened, so I plugged in the DVD player to continued my study of “complex adaptive systems” of which naturally evolved systems are evidently a subset – Subset? That doesn’t make sense. How can a factual natural reality be a subset of a human conceptualization???? Ahhh, I get it. If your head is in the Biosystem world view, the naturally evolved complex adaptive systems are a subset of the Biosystem. On the contrary, if your head is in the corposystem world view, you are required to behave as though all of the natural world is a subset of human conceptualization.

Not long now, we will have to choose sides or lose the field of play.

160320-SantaFe-asc_3631RLsI did that. One day in 2006 I sat at the end of my driveway in my old white Ford pickup and realized that we cannot solve our human problems from inside our corposystem worldview that created the problems. I decided then and there, ten years ago, that I would approach my life from that time forward trying to think like a system. As though I were a system. And it has been difficult even for me, with all the background that I have in my life as a scientist and a human person, to get my human head around some of the Biosystem needs for its survival.

So it’s hard, but that is an entirely different subject that has nothing to do with the fact that we will soon have to choos. In fact, we are choosing every day — with everything we do. What do we want more – compassionate recognition of the effect our behaviors have on other people and all sentient beings? Or, like a child, do we want what we want — no matter what?

This is Bare Bones Biology, a production of FactFictionFancy.Wordpress.com.

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Bare Bones Biology 305 – Survival

As the processes of Life proceed through time, each in intimate relationship with its environments, change happens. Life changes over time. I think you already know this, but that is not the interesting part of the story. It is not the system itself (for example, the Human species as a system, or the power that we humans wield, or even our individual commitment) that generates the change over time inside some specified environment. Rather, the environment imposes change upon the system (for example us). And the result of this “dance among the systems” determines which systems survive. We do not need to fight for survival of our system — we only need to know what is required of us to enhance to coalition of all the naturally evolved systems – and do it.
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However, this is not usually what happens, because naturally evolved systems most often do not change course. They usually become more and more of whatever is their primary specialized attribute, until the system collapses, and some new baby system arises that fits itself neatly into a nurturing niche within Life.

 

This is because a naturally evolved system is set up to protect itself from change. Its prime directive is to perpetuate itself, and all the little bits and interacting pieces of the system do just that. For example, consider the corposystem as a model, because I have already used the giraffe so many times it becomes boring. The corposystem is set up, organized, naturally evolved to perpetuate itself by making money through growth and making growth through dominance. This is what all its bits and pieces (let’s say all the people trained in the American TV dominated educational system) are set up to do.

 

That’s different from giraffes, because it is the genome of the giraffe that is set up to grow a long neck to interact with an environment of treetop browsing. But we are not talking about genetics or giraffes, we are talking about naturally evolved systems, and the corposystem is a naturally evolved social system composed of people in their environment.

 

Because the function of any system is to use its parts to maintain itself, and because of the amazing success of behaviors – therefore it is in large part human behaviors that maintain the corposystem.   And what directs human behaviors? For the most part it is the human world view that directs human behaviors. Humans born, raised and trained within the corposystem educational system maintain the corposystem world view by their behaviors.

160316-Bruan-160316-bryan-asc_3574RSs

Now along comes a threat to the survival of the corposystem worldview of growth by domination for gain. What is the threat?

 

Overpopulation. Physics. Energy. Growth is impossible beyond the ability of our Bios to feed us. And we cannot change physics or energy. They are what they are.

 

Still, the function of a naturally evolved system is to maintain itself, and the only way it knows how to do this is to use its imprinted (evolved, educated, inherited) worldview.

 

So we try harder and harder to grow – and more violently to dominate – until we are destroying other naturally evolved parts of the Bios — and that changes the Bios from a cornucopia of biological wealth to a dessert of thirst and hunger.

 

And what will happen if you try to have this conversation with a citizen of the corposystem?

 

The function of a biologically evolved system is to maintain ITSELF.   That does not mean to survive. It means to be what it is at any cost, and when the environment in which it can flourish changes, as we have changed it, the cost is, indeed, our survival.

 

Because that is how evolution functions. That is the process by which naturally evolved systems interact with their internal systems and environmental systems to generate viable complexity.   By killing off the parts of the system that do not contribute to the viable complexity of the system.

 

This is Bare Bones Biology, a production of FactFictionFancy.Wordpress.com,.

 

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Bare Bones Biology 304 – The Frame

All of our universe is composed of naturally evolved systems. I am a naturally evolved system; I am one unit of the human species that is also a naturally evolved system that consists of nearly 8 billion units and their environment. The corposystem (a social system) has evolved within the human species and is now our primary paradigm. The corposystem and the human species and I are all part of the naturally evolved Biosystem, which is a much more ancient and powerful naturally evolved system — but the Biosystem is not human. The Biosystem is a highly evolved natural system that consists of many “levels of organization” that all and each are naturally evolved systems.   All of this intricate naturally evolved balancing act involves interactions of many kinds among and between the systems at multiple levels.

160325-chaos-asc_3723Ss copy

Evolution is not primarily about survival of the fittest, and it is not primarily about objects such as ourselves. Evolution is primarily about energy and information relationships among collaborating systems.

 

“Survival of the fittest” is a pitiful, woefully inaccurate meme that has damaged our creative response to Life as it is, and precluded our insights.

 

We humans are not at the top of that peak or any other, nor can we be. We humans exist at the level of individual organisms. We are composed of naturally evolved systems (example, the nervous system) and the systems are composed of naturally evolved cells.   If cells had not evolved, then a nervous system could not have evolved, and the various species of organisms could not have evolved. Thus the real world of naturally evolved systems is much more complex than four dimensions the physicists work with, or even the multidimensional approach to a mathematical description of the quantum world. It is very difficult to imagine. But it’s more worthwhile and less embarrassing than to use our naturally evolved brain to think in ignorant meme-imposed frames.

 

The real world consists of naturally evolved systems that interact with each other to generate more complex naturally evolved systems. The history of our Creation lies in the ability of these systems to function at all the systemic levels cooperatively so that I am alive because all my cells and organs and organ systems are alive and functioning together cooperatively to generate and maintain me; and my species, Homo sapiens maintains itself as a naturally evolved system so long as it generates (evolves) social systems that are beneficial to us all, and so long as those social systems also benefit the ecosystems of which Homo sapiens is a part.

 

What that means is:

 

1 – the naturally evolved ecosystem is the cutting edge where our species (at present our corposystem) gracefully submits to the needs of Life itself to maintain and support ALL THE LOWER LEVELS OF LIFE that are essential for the survival of ourselves and of the whole Biosystem – or not. Natural selection is the name we have given to that process of success or failure.   Either we fit our behaviors into the requirements for the maintenance of life of our environments — or humans do not survive, nor will any of the naturally evolved systems of which we are composed. This is how systems sustain themselves; if we can’t get with the program, we aren’t welcome in the game.

 

2 – if we succeed in aligning our behaviors with the ecosystem of which we are a part — so that we contribute to the welfare of that ecosystem and the entire Biosystem, then we can survive. If not – not.

population-environment

3 – Right now, Homo sapiens is dying because Homo sapiens is an unfit species that is destroying itself by overpopulating. Overpopulation events of any species normally do change the environment of that species. THAT IS HOW SURVIVAL OF THE FITTEST PRIMARILY WORKS! The unfit species destroy themselves by their inability to survive within the environmental changes they themselves have generated.

 

4 – If we continue to believe we are in charge of our environment, rather than the other way around, we destroy one huge opportunity — that sublime evolutionary breakthrough, to the next higher level of reality that could lead to a sustainable human future. We cannot do this by telling the ecosystem how it should function within The Life.

 

If we choose a sustainable life style for our grandchildren, we must live within this frame (paradigm/worldview). We could do it tomorrow, if we were willing to face our problems with courage rather than anger, fear and denial — and to inform our human compassion with the wisdom of Life and Death.

 

 

This is Bare Bones Biology, a production of FactFictionFancy.Wordpress.com. A copy of the podcast may be downloaded at:  http://traffic.libsyn.com/fff/BBB304Untitled_Multitrack_1.m3

 

 

Definitions and Descriptions (we can probably improve these definitions):

 

Energy is classically defined as the “ability to do work’ using the Laws of Thermodynamics that study work and entropy. Work can be thought of as the cause of change, movement, or organization.   Entropy can be thought of as disorder or disorganization in the states of Energy and of Information.

 

Another modern description of entropy, Seth Lloyd. 2006. Programming the Universe. Alfred Knopf., page 191: “You can think of entropy as consisting of random junky bits and negentropy as consisting or ordered, useful bits.”  

 

Information was described by Claude Shannon as: “Information (theory) . . , though related to the everyday meaning of the word, should not be confused with it.”   And: The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point.” (Quoted in The Information, chapter 7, Information Theory, by James Gleick, pub. Pantheon.

 

The word communication, when applied here to naturally evolved systems refers to whatever processes may share information across whatever physical, social or functional boundary may separate the systems, for example the cell membrane, human skin, ecosystem climate zones, tribes, languages, species. These boundaries may be seen to represent the evolutionary history of the entity or organism, as for illuminated by levels of organization, an insight brilliantly proposed by Lynn Margulis in her lifetime, and the prior concept that “ontogeny recapitulates phylogeny.”

 

Naturally evolved systems are self-organized, self-perpetuating units that consist of nodes and processes. Neither the nodes (objects, for example ourselves) nor the processes (any example will do, from gravity to hydroxylation) nor the environment in which the nodes and processes function (the environment is composed of other systems), none of these is paramount, though the environment is the most powerful, and all of these levels of systems are involved in the cyclic language of Life that evolves (adapts) and perpetuates itself by collaboration with other systems as it spirals through time.

 

 

 

 

 

Bare Bones Biology 270 – What If?

“If we surrender identity over time, we give up on the existence of things.”

Professor Steven Gimbel, Redefining Reality, The Great Courses.

He means a thing, any thing, maintains its “self” over time. That is his definition of a “thing.”   Any object that retains itself over time. Thus, we are all things, because we “maintain our identity,” that is we are ourselves, throughout our lives. After which we are not a thing, or at least not the same thing that we were when we were alive.

My definition of a thing is more like something that occupies space and has weight. That’s a version of the physicists’ definition of matter. Without playing physics games, “things” occupy space and if they step on a bathroom scale on earth, the needle goes up.

150818-chamadays-ASC_9055RLSsOf course, that is not the entire definition, because we know that everything (every thing) also involves energy. Energy, at our level of LIFE, is not matter. Energy is the ability to do work, and work is change. So energy is involved with change of one kind or another.

Thus it must be that, everything on earth, including the corposystem and us, is a complicated combination of thingness and energy. You are a thing that can use energy to make change. You can even decide what changes you want to make. You are a thing that uses energy as a tool. To get what you want.

Right! But are you sure?

What if it is not we who are using energy as a tool; but what if energy is using us as a tool? What if the energy processes of LIFE are more important than the forms (things) such as ourselves? What if your body is only a thing, like a refrigerator for example, that stores and maintains processes. And then, later, when energy has saved up enough different kinds of processes, it can use those processes for something more important.

Perhaps all the energy in the Biosystem is involved in the humongous Energy Project by evolving new processes and storing them in living “things.” Like us. The Energy Project has been evolving organisms in which to perpetuate those energy processes – just keep them going until the Biosystem can collect all the different processes it needs to make LIFE perfect? What if the collective energy of the Biosystem decided to evolve humans so we could understand its Biosystem Energy Project? Maybe even help bring it to fruition – to make the perfect LIFE.

If so, it was a big mistake. The reality is at the present time the corposystem has taken control of our individual and collective human power, and is using our power to attack and try to dominate the LIFE of Earth by overgrowth of our species and our economy.

If you were energy using the laws of nature to grow a perfect balance of LIFE processes on Earth – what would you do about these very imperfect humans who are trying to take control of your project and use it to make money instead of making LIFE more perfect?

Humans are not the center of the universe. That’s one thing we do know for sure. The universe can get along without us. It did for billions of years. It might be able to get along better without us.

Probably all those questions above aren’t true, because LIFE is not a question of things versus energy. It’s more a question of keeping everything in balance. Much more. Nevertheless, if I were making a personal vision statement, I believe I would take these questions seriously. After all, we do not really know the answers to any question. Not for sure. Not if it’s a question about the entire Biosystem or the entire Universe.

So, if I were making a personal vision statement, I think I would go out of my way to include the statement: “Do No Harm.” And then I would think hard about how the Biosystem Energy Project defines harm. As compared with what the corposystem has taught us to believe.

 

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

 

A copy of this podcast can be downloaded at:

 

REFERENCE

Professor Steven Gimbel, Redefining Reality, The Great Courses.

Bare Bones Biology 218 – Systems Evolution

Dear Friend —

Can you believe it? Here is a quote from a Taos (New Mexico) photographer, referring to the northern section of the Rio Grande river: “Watching visitors experience this sight is always entertaining. They seem to lose all sense of reality in the face of its grandeur.” Taos summer visitors guide 2014. This photographer, lives right in the middle of the grandeur, and he believes it to be – what? A movie prop?

But never mind our brainwashed young, today I absolutely planned to talk about my interaction with —let us call her Amanda—, but the following is what came out of my fingers when I sat down to type and three ideas came together in my inbox:

First – Your comment that most people cannot imagine a world without the energy of oil (see ref A below). This is true. And there are many other important things that most people can’t imagine. You can. That is why I picked your project to support, in my small way, out of the hundreds I have looked over in the past 15 years. —Amanda— can also imagine, though not yet as deeply, because she is much younger. So she is the other I support. I mean enough to stop what I’m doing and think about what y’all are doing. Of course, I have seen a number of other people with this kind of imagination, but without projects to which I could contribute usefully. Not unless they would ask the questions.

Second – I think the creation of a central dogma of imagination is one of the ways (maybe the major way) that our corposystem prevents discussion of critically important dissenting ideas (or any dissenting ideas, but now is critically important to our survival). It’s pretty much what “1984,” the book (B), is about. David, for example, used an elegant corposystem-imposed method very effectively to disempower discussion of biological reality.

I am not saying that David, or someone up there in the corposystem, is telling us not to talk or think about (something). Of course, they are to some extent, but more importantly I believe lock-step thinking is part of the biology of what maintains human systems, while outside-the-box thinking provides the variability necessary if change is to happen.

The Law of Life, generating novel systems by recombination, is how evolution brings about change, but once you get a viable combination of traits together in one system, and that system fills a niche it can feed upon, then that combination of traits is maintained essentially changeless until the system dies. To survive, the system must protect this unique combination of traits, so it does not change; rather, it becomes more and more of what it is. Whether the system be the longer and longer neck of a giraffe, or the growth fixation of the corposystem, the primary function of a system is to maintain itself.

I believe behaviors such as co-dependence are at root biological imperatives that serve similar social functions. Easier–to-recognize examples, such as the glass-half-full-syndrome

https://factfictionfancy.wordpress.com/2009/05/21/the-glass-half-full/
‎https://factfictionfancy.wordpress.com/wp-admin/post.php?post=725&action=edit – post_name, https://factfictionfancy.wordpress.com/2013/11/07/
bare-bones-bio…a-quarter-full/,

and the nice-speak syndrome (https://factfictionfancy.wordpress.com/2013/06/25/bare-bones-bio…156-nice-speak/) (again, see “1984”), similarly protect human systems from outside ideas. Even ideas that would prevent massive human suffering but also would, inevitably, change the system. The corposystem is not only a business plan – it is an evolved biological system that operates just as evidently out of the Law of Evolution as do physical systems.

Third – I also believe there are physical reasons for our human disinclination to imagine or talk outside the model required by the system. Outside the box causes intrinsic biological pain to humans. http://www.bbc.com/future/story/20140514-how-extreme-isolation-warps-minds

In sum, the function of a system is to maintain itself, and that is also the simplest way to describe the Law of Evolution. I see it everywhere within our corposystem, equally as I see it in the tree of Life and the development of the whole universe. I think it is a natural law more basic than any other we have described so far.

So what do we do about this in a culture that defends itself by finding ways to not discuss the issues?

My answer is to speak as truthfully as possible (https://factfictionfancy.wordpress.com/2013/08/20/ factfictionfancy-130820/), trying to balance the long-term and short-term benefits to the individual, who is usually me; the culture, which is the corposystem; and the needs of the Biosystem, which we all require for our survival. At the same time I have usually tried to avoid being lynched (or crucified) for challenging the system at it’s weak links. The goal is to shake up the corposystem world view by challenging demonstrably false statements/world view (https://factfictionfancy.wordpress.com/2013/05/01/bare-bones-bio…3b-world-views/), so as to make it possible for people to think about the content rather than the package in which it is wrapped – to loosen a chink in our world views — while at the same time avoiding unnecessary unkindness and/or revolutionary violence, which is what will happen if the goal fails.

There is the very remote chance that humans can pull through this biological crisis because we have two unique advantages that no other species has ever had. 1) We can think, when we choose to do so. And (2) the information is available to us, whenever we decide to use it for the benefit of all sentient beings.

This is Bare Bones Biology, a production of FactFictionFancy.Wordpress.com and KEOS radio 89.1 in Bryan, Texas. The audio copy of this blog is available at:

I have nothing much to lose. So – that’s what I do. I have tried it both ways. To conform to the system merely empowers the system — without fundamentally changing it – because systems are flexible and can co-opt challenges, as ours has done with the charitable activities, to use the challenges to empower the system itself. Very clever. But I don’t want to empower our toxic system. As I have said from the beginning, my search is to find behaviors that will not make matters worse. And I believe that can be done only by not participating in it. That’s not possible, so one participates as little as is possible.

The greater good is compassionate honesty, with the goal in mind of reducing suffering of all sentient beings — not only us. And I think at least Tibetan Buddhism, at least the Dalai Lama, has made some fairly strong statements about wise compassion, and about education toward reality, that conform with this view. (Not the view about evolution, of course, I think he is unfortunately not well informed in this area, but about wise compassion. And he is clear that wise compassion requires education. And effort.) (D)

REFERENCES ‘
A) Kelly J. Ponte, PhD. “Retaining soil moisture in the American Southwest. Sunstone Press, Santa Fe NM. (p19) “Humans do not need oil to live. Oil makes our lives more convenient. Water makes our lives possible.” Let’s all try to imagine a world without water available to humans and how it is coming to be. The information is available and you can think.
B) George Orwell, “1984”
C) Links
https://factfictionfancy.wordpress.com/2013/08/20/factfictionfancy-130820/
https://factfictionfancy.wordpress.com/2009/05/21/the-glass-half-full/
https://factfictionfancy.wordpress.com/wp-admin/post.php?post=725&action=edit – post_name
https://factfictionfancy.wordpress.com/2013/11/07/
bare-bones-bio…a-quarter-full/
and the nice-speak syndrome https://factfictionfancy.wordpress.com/2013/06/25/
D) – Bikkhu Bodhi, translator, “In the Buddha’s Words,” Wisdom Publications, Boston

Writing this blog has also moved a chink in my world view. I have been thinking in the back of my mind (corpo-think) that we could “move” the corposystem toward intelligent imagination by educating the masses to understand the implications of the Law of Life. Now I’m reading of the Buddha’s wisdom as translated by a Theravaden Buddhist, with a forward by The Tibetan Buddhist. Apparently, that was one of The Buddha’s insights – that we cannot educate the masses away from their world view (because of the many ways in which a social system protects itself from change, mentioned above but he didn’t know the Law of Life). He finally concluded that every person must address this responsibility for herself, and that seems to be most of what he talked about to householders. Well, looking at the imaginations of our recent generations of well educated young householders – and the fact that more children are born every year than we can possibly influence, and immediately indoctrinated into the corposystem world view – what do you think? That’s the problem with a system. It is more powerful than an individual, even if she is right.

Thistle in Bloom

The moths, butterflies, flies and ants are eating and courting on the thistle blossoms. The hummingbirds got here too early. Last year we had hummingbirds eating and nesting in their embrace.

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In a stable, sustainable culture, one of the most amazing phenomena is the way that the thousands of life cycles mesh with each other, regulated in large part by the climate, so that the creatures are born when the food is available.

Bare Bones Biology 204 – Gary’s Question #3, Evolution and Emergent Properties

Our goal is to build a human system (society) that is sustainable and reasonably comfortable within a healthy Biosystem. (Bare Bones Biology 195, http://FactFictionFancy.wordpress.com/2014/03/12/). That is reason enough to learn everything we can about the Law of Life (that is, the Law of Evolution and the many interacting processes involved with Evolution) Bare Bones Biology 197, http://FactFictionFancy.Wordpress.com/2014/03/26/6601

140513-canyon-ASC_9026RLSs copyThis series of podcasts, beginning with Bare Bones Biology 194 http://FactFictionFancy.Wordpress.com/2014/03/05/6548/ is meant to provide the most basic overview of the Law of Life, one of the laws of nature, along with the laws of thermodynamics, gravity, etc., that operate to maintain Life on Earth. That means Life itself. It does not mean human Life. Humans could not survive without the other parts of the system of Life on Earth. The earth will still be alive 50 years from now, but it is not clear that humans will continue to be a part of the Biosphere. It is the Law of Evolution that supports the positive biological systems and disposes of those that have negative impact upon the viability of the Biosystem (Bare Bones Biology 194, http://FactFictionFancy.Wordpress.com/2014/03/21/)

Both the Biosystem and the human corposystem are systems. Systems are self-perpetuating, so long as they maintain their positive interactions with their environments, and each system grows around a set of core properties that together have a unique survival value within the Biosystem.

Six of the most basic requirements for Evolution to function positively are described in Bare Bones Biology 198 (http://FactFictionFancy.Wordpress.com/2014/03/30/) and Bare Bones Biology 199 (http://Fact/FictionFancy.Wordpress.com/2014/04/08). They are:
1-Reproduction; 2-Death; 3-Inheritance of traits; 4-variability of traits; 5-transmission of traits to the following generation; 6-Interconnectedness of processes and “things,” or
objects. (Objects are organisms, cells, tissues — all the objects that are generated at all the levels of organization of Life and are maintained by the processes of the Life system). (Bare Bones Biology 199, http://FactFictionFancy.Wordpress.com/)(Bare Bones Biology 200, https://factfictionfancy.wordpress.com/2014/04/17

140513-canyon-ASC_9028RLSs copyThere could be no Life without interconnectedness because there would be no way for the living objects to change in response to their environment. There could be no systems without interconnectedness because the function of a system is to maintain itself in the face of its changing environment. If the system cannot maintain itself as the environment changes, then it fails (dies), as our corposystem is now failing. It is the Law of Evolution that imposes the necessary balance between the need of a system to respond to its environment and the system’s necessary tendency to avoid change. (Bare Bones Biology 196m http://FactFictionFancy.Wordpress.com/2014/03/21/ )

Response to environment in lower systems (individual cells or individual organisms) happens using physiology. This is the first function of the information encoded in the genes, or DNA (https://factfictionfancy.wordpress.com/2014/04/22 ,Bare Bones Biology 201). Many or most genes that are doing this first function, regulate processes that generate a living thing thing or object, such as yourself, or a tree, or a cell, or a kidney, by responding to the environment
embryologically or physiologically.

Response to environment in the higher life forms (species; ecosystems; the Biosystem) happens using Evolution. The nature of Life (the living objects at all the levels of organization (https://factfictionfancy.wordpress.com/2009/12/07/) results from balancing the needs of all the interacting systems as they respond to their internal and external environments (Bare Bones Biology 200, http://Fact/FictionFancy.Wordpress.com/2014/04/08). The function of Evolution is to maintain this balance.

Depending upon all the above factors, and more, the evolution of life forms responds to the environment in multiple ways, from very slow, step by step evolution to remarkably rapid jumps known as biological saltation or punctuated equilibrium (ref Wikipedia). This part of evolution is possible because of inheritance of traits that can be passed on to the next generation, and it is the second function of DNA — to make exact copies of itself (all the genes) to be passed on to the next generation in the sex cells and by fertillization (ref Wikipedia). The genes then use their first function in the new gamete by activating the processes that create new living “things” (cells, organisms, tissues, etc.). Evolution does not act directly upon the genes; Evolution acts upon the variable characteristics (phenotypes) of the things (organisms, tissues, cells, etc) that are created by the genes.

A small amount of genetic and phenotypic variation results from individual gene changes, or mutations. More results from many, many genetically controlled processes that work together. For example to make a jaw bone, or a tooth, tissues that interact with each other, requires many genes interacting with each other and with the embryonic environment in which the jaw is made. Variability of inheritable traits is necessary for Evolution, and the genes encode the traits. Therefore genetic variability is an important pre-requisite for phenotypic variability, and there are many processes that generate genetic variability, from meiosis of the sex cells in individuals to the maintenance of subtle genetic errors in the gene pools of species. We discussed these in (Bare Bones Biology 201 – https://factfictionfancy.wordpress.com/2014/04/22/)(Bare Bones Biology 202 https://factfictionfancy.wordpress.com/2014/05/01/)(Bare Bones Biology 203 – http://FactFictionFancy.Wordpress.com/2014/05/09).

In all the millions and millions and billions of recombination and mutation events of genes, very rarely, some call it a singularity event, a unique COMBINATION OF genes—that encodes a unique combination of processes—comes together to generate, suddenly (on a geological time scale), an emergent property – a new functional sustem that sustains a new emergent property that provides a new and different way to survive: eating, flying, swimming, growing, a new way that can populate a whole new niche in the environment. This is a big jump in evolution; certainly it happens, probably it is what we refer to as punctuated equilibrium or saltation — and then it is followed by adaptive radiation.

However, unless you intend to live to be a million years old or so I would not wait around for a singularity event to save us from our own hubris (Bare Bones Biology 195, http://FactFictionFancy.wordpress.com/2014/03/12/). So I would suggest – instead of playing human mind games — that you join in the reality-based effort to sustain a Biosystem humans can live in — by using your talents to dig as deeply as you can into understanding and teaching the real Facts of Life and helping to discover how we can learn to submit to them by living sustainably. Rather than try to negate the Facts of Life based on your personal opinions. If you were to succeed – then what? No life.

On the other hand, if we could learn to conform ourselves to reality, we could conceivably build a new human social system with a different set of core properties – combined to form a new emergent understanding of Life — that are sustainable and provide reasonably comfortable life style for humans on a viable, living earth.

Win or lose, that is the most important effort that any human person could make.

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

The podcast of this episode is available at:

Bare Bones Biology 203 – Gary’s Question #3, Genetics

The process of evolution results in a change in the gene pool over time so that each species separately and the entire ecosystem, if it can respond to its environment, can stay alive. The ability to respond to the internal and external environment is the definition of being alive and of being a Life form, whether a cell, or an individual organism or a species or the entire Biosystem. That the Biosystem is a life form is not an opinion; it is a fact, or if you prefer, a definition.

140506-flowers-asc_8951SsIt’s also true that inheritable mutations are not altogether random, but we are not talking about mutations here, we are taling about evolution, and as I tried to explain previously in this series (Bare Bones Biology 201 – Genotypes, Phenotypes and Evolution), evolution works on the phenotype, not the primarily the genotype. The genotype is all the genes in one individual organism: the phenotype is the sum of the physical characteristics of an individual organism: Evolution is a change in the gene pool of a species (not an individual, that is impossible) over generations of time: the gene pool is all the genes in all the individuals of the species or of the ecosystem.

The process of natural selection, which is part of evolution, selects FOR survival and reproduction of phenotypes that function well in the environment. If and only if that genotype is heritable, then the entire gene pool may be change to favor one gene or, much more likely, a combination of genes, that are best suited to whatever environment is operating at any given time.

It makes no difference to evolution whether or not mutations occur, what those mutations may be and whether or not mutations are random. Evolution does not select genes; evolution selects phenotypes that function well within the Biosystem at any given time and place.

The function of the genes has primarily to do with the survival of the individual and of the species, and it is two-fold. First, the genes turn on and off during growth, development and survival in response to cues from the environment. These actions are studied by cell biologists, physiologists, developmental biologists. This level of activity is what you referred to as epigenetics – that is how genes know what is happening in and around your body so they can activate the appropriate responses. This is how we stay alive, day to day. It does not change the genes; in fact the basic function of the genes is to not change but to provide the information necessary for the organism to respond to environment, and the second function of the genes is to pass on all of that information to the next generation without changing the genes but reorganizing them, so that each individual has a slightly different phenotype. The variability of the phenotype is the connection between the genes and the process of evolution.

The most common kind of genomic variability is recombination of genes. Recombination ensures that every individual organism in a species is slightly different from every other organism in that species. Another way that variability is generated is by mutation.

140506-flowers-asc_8953SsGiven that every cell in the body has a full set of genes, and all these genes are copied billions of times, it is not surprising that mistakes (mutations) occasionally occur. It would be surprising if they did not. Some of the mutations can be passed on to the next generation. Therefore every organism does have a small percentage of mutations and every species carries a large number of mutations in its gene pool; should any of these ever become useful to the survival phenotype of the species – evolution will select for those mutations.

This whole story of nested processes is the language of Life, as it has been created. Unlike the languages of man the Language of Life is completely honest, and yet it is far, far more mysterious and empowering and glorious than the concept of personhood, which places God and his works subordinate to the narrow mind of man.

To download the podcast of this blog:

This is not yet the end of the story. I’ll talk about punctuated equilibrium next week.

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

Bare Bones Biology 199 – Evolution

In Bare Bones Biology 198 (https://factfictionfancy.wordpress.com/2014/03/30/) and in the blog that was posted to FactFictionFancy the following day (https://factfictionfancy.wordpress.com/2014/03/31/yesterday-2/), I listed six characteristics of all living things that make them responsive to the world outside of their own bodies.

That is an important definition of Life. Life and living things are responsive to the environment, and their environment is everything that is outside their own bodies. They are also responsive to the internal environment, which is everything that is going on inside their own bodies. Within physiological limits, Life is able to respond to change. If it can’t – it dies.

Most people notice this and think it is ordinary – of course — ! It is ordinary to us. We are alive. We eat, we walk, we talk, we try not to run in front of cars. But in the universe, so far as we know, the interconnected systems that can reproduce their own kind and recycle the materials of which they are made, and find food and use it to do those things – this is not ordinary.

110825droughtasc_3018sls-copyIt was the greatest and most marvelous event after The Creation itself, when a group of processes came together, to form a unitary system that was able to respond to the environment by moving toward food or moving away from noxious things. It was the creation of Life. Life is a system composed of a set, or sets, of processes that function to respond to the environment in which it lives by reproducing its own kind.

Six qualities that make life possible, that I listed in those last two blogs are: 1- Inheritance of traits; 2- Variability of traits; 3- Reproduction; 4- Death; 5- Transmission of traits to the following generation; 6 – Interconnectedness of the processes of one living system with all the other living systems on earth.

Those qualities are essential for all living systems and their subsystems — all species – to maintain Life on Earth. And the original “invention” of Life was the coming together of a group of processes that maintain life by responding to the environment in which they live.

Evolution is the Law of Life on earth; Evolution makes Life possible because Evolution is how Life responds to its environment. Without evolution there could be no Life as we know it on earth, because Life and living things must be able to respond to their environment or they could not stay alive. Think of the first breath of air that a newborn infant inhales. Think of the color of your eyes, or of your skin, that you inherited from your grandparents, or great-grandparents. If there were no evolution, Life could not respond to conditions in the environment and there would be no Life.

A living thing is a system that is able to respond to its environment to find food, water, air so that it can reproduce itself and continue staying alive generation after generation. It is the natural Law of Evolution that guides and balances all these processes of Life (and a myriad more) within all organisms and between all organisms and all other systems on Earth as the entire interacting set of systems continues to use the energy from food to respond to the environment and so to stay alive.

Evolution is NOT primarily survival of the fittest. Evolution is the natural process that permits living systems to respond to their environments and so to maintain and BALANCE all the processes that are required for living systems to stay alive — including life and death, reproduction, using food energy and cycling the water and nutrients through the whole interacting set of systems and subsystems. Therefore – if you still think of Evolution as “survival of the fittest,” or any other sound bite that is more simplistic than the holistic balancing act that Evolution actually is, you cannot understand climate change, and regardless if you are one of the bad guys or one of the good guys – if you win or if you lose — you cannot help to make wise plans for the future of humans on this living earth.

This is Bare Bones Biology, a production of FactFictionFancy and KEOS FM 98.1, Bryan, Texas. A copy of the podcast can be downloaded here: http://traffic.libsyn.com/fff/Bare_Bones_Biology_199B_-_Evolutiona.mp3

Yesterday

In Bare Bones Biology 198 https://factfictionfancy.wordpress.com/2014/03/30/ I said that
Evolution is the process of change in the gene pools of species over time. A species is a particular kind of living thing and its gene pool is all the genes in all the individuals of that species.

The function of the process of evolution is to maintain Life. This is done by balancing the following characteristics of living things:
1. The inherited physical and behavioral characteristics of organisms (living things) are transmitted by the genes from one generation to the next.
2. Every living thing is a least a little bit different genetically from every other living thing;
3. In all species, more offspring are born than can survive because long-term there is not enough food available for them all to survive.
4. The genes of those that do survive are passed to the next generation.
5. Individual organisms do not evolve. They can change, but evolution is the difference between the gene pool of one generation and the gene pool of the next generation.
6. The entire Biosystem evolves all at the same time together.
The function of the natural Law of Evolution, the basic Law of Life, is to maintain LIFE by mainaining a viable BALANCE among all the interacting factors at all the many levels of the Life on Earth.

The next question is – what is a Level of Life.? And how do they interact?

Levels of Organization of Life

https://factfictionfancy.wordpress.com/2009/12/07/levels-of-organization/

The Biosystem is a Network of Levels of Organization

The diagram below needs explanation, but it won’t be easy, because the Bosystem is so complicated that it is impossible humanly to represent or to fully understand.
If you find it mind boggling to comprehend the levels of organization, all interacting among and between themselves, then you are just like the scientists, the politicians, the religious and everyone else. Fortunately, we do not need to understand all the little details of the system in order to have a good idea of how it functions — the structural and functional requirements for it to stay alive — and that is our goal. A basic appreciation of the beautiful idea of networking. and of the levels of organization, is background for understanding the flow of energy, and of other things, through the living ecosystem. Life is possible because of the internet of living and nonliving things through all the levels. The basic format of these realities is outlined in the below diagram.

The ecosystem consists of sets and subsets of living and nonliving entities that interact between and among themselves. We can not represent the entire system in a diagram for two reason. One is that the sets and subsets (levels of organization)
are flexible, a fact that is necessary for their survival (sustainability). The other is that there are just too many interactions to understand or represent.

For example, looking to the diagram, there are ecosystems within ecosystems. I am a functioning part of the pasture ecosystem and the East Texas group of ecosystems and in fact all the ecosystems in the world because I contribute to the materials (such as carbon dioxide) and the energy flow and many other activities that occur within each of these ecosystems and the whole earth ecosystem. If I could draw all the lines of interaction between myself and all the other ecosystems and all the other levels of organizations, the entire page would be black. So I drew only one or two or a few lines to feebly represent just a few interactions.

Imagine that everything interacts with everything on this diagram in some way(s) and also everything interacts with millions of other entities that make up the living system. For example, your heart interacts with every other component of your body; your resilience and therefore your survivability (sustainability) would be unlikely if any of these interacting components of your body were missing. All the organs work together to maintain your life. This is represented by the lines between the heart and kidney and skin on the diagram. However, it is true of every organ in your body. They all interact. Similarly, the leaves, bark and other organs of a tree all interact with each other to make the tree alive, and the tree interacts with nearly everything else in the ecosystem, including us.

We are only one component of the metabolism of the ecosystem. Our lungs breathe the oxygen that is provided by plants; our food gives us the energy we require for life; the environment degrades our wastes, so that we are not suffocated in a dung-heap of the unused byproducts of our metabolism, and these byproducts are re-used by other organisms. These processes are carried out by other organism that all are interacting within all the big and little ecosystems of life on earth. We could not survive without the other elements of the ecosystem, and we also contribute to the other elements of the ecosystem.

Levels of organization are shown on the diagram by the large headings on the left side of the page. Levels of organization are a special type of interaction that we have discussed before. Everything in the universe is composed of other, smaller things. These relationships are referred to as levels of organization. A very few example relationships of this kind are shown in the diagram with vertical lines. To summarize some of the levels of organization that exist:

1-The whole earth ecosystem is made up of smaller ecosystems and organisms. The whole earth ecosystem is the biggest (most inclusive) organized level of Life on earth.
2-Organisms are made up of organs and their environment
3-Organs are composed of specialized tissues and their environment.
4-Tissues are composed of specialized cells and their environment
5-Cells can be organisms or they can be subunits of organisms. The cell is the basic unit of life. Below the cellular level of organization, life as we define it is not present in the interacting systems of which it is composed. However, obviously, are also necessary for Life to exist because living things are composed of them.
6-Cells would not be alive without the precisely organized organelles, macromolecules and molecules of which they are composed.
7-Organelles are subunits of the cell that perform specific functions. For example, the chloroplast is an organelle that is made up of macromolecules and molecules that, in the environment provided by the cell can do the processes of photosynthesis. Photosynthesis is the process of changing light energy to chemical energy that is used to form the energy bonds of macromolecules.
8-Macromolecules are organic molecules joined together with other molecules by energy bonds.
9-Molecules are made of atoms that are joined together in very specific ways by energy bonds. The kinds of energy bonds and the kinds of relationships between the atoms are not random. They depend upon the fact that different kinds of atoms have different characteristics.
10-Atoms can not be seen or directly measured individually. However, if we collect a few million/billion atoms of the same kind, all together in one place we would call that an element. There are not very many elements that (in their special combinations as molecules) make up all the living and nonliving things of the ecosystem. These elements/atoms are diagrammed by chemists in the “periodic table.” A lovely book by Theodore Gray and Nick Mann describes and illustrates all these basic elements (and atoms) of our existence.

Atoms are studied by physicists. There are many metaphoric descriptions of atoms, but the bottom line is we do not fully comprehend atoms from our perch so much higher up in the levels of the ecosystem (just as we do not fully comprehend things that are at levels of organization over our heads. Our sensory organs are designed to function in our own level.) What we need to know is that atoms are matter (they have mass, which means they have weight and volume. Everything from your desk to your grandmother is composed of atoms). Atoms also carry the energy that we require to do any kind of action in our lives or in the ecosystem. The energy of atoms determines how the different atoms can make energy bonds with other atoms so that molecules can form, and macromolecules, and organelles, and on up the levels.

It is important to know that humans do not understand most of these interactions. It’s also important to remember that any system that has more interactions, to a point, is likely to be more resilient (suggested reading linked by Albert-Laszlo Barabasi). Resilience is largely the result of complexity and is essential to life. Increased complexity of a network increases resilience because it makes available “fail-safe” options by providing several methods of accomplishing each process. Increased complexity can also increase the efficiency of energy usage (notice these elements also can be true of social organizations).

However, this does not mean that more complexity is always better than less complexity. Complexity is not the only element of life that is essential, and complexity must be maintained in balance with all the other essential components of ecosystem viability. Too much complexity can be as harmful to the balanced organization of a network as too little complexity. We could not be alive if the nature of the chemistry and physics of our environment were different than they are, or if the interactions within the ecosystem ceased to function. All the levels and all the interactions make us what we are.

Evolution not only functions to maintain balance among all these levels of Life.

Evolution also created at least some of them.

It is my personal opinion that the process of Evolution is so basic to existence that it is probably responsible for creating all the levels.

And only God could create the process of Evolution. But I don’t see any reason to argue about those last two points, because it is not our job to determine how the universe functions.

Our common goal and our human responsibility to God and to each other and all sentient beings is to individually and collectively do our very best to pass on to the seventh generation of humans yet to come a sustainable, reasonably comfortable human culture within a healthy Biosystem.