LifeOS: exploring the system that executes DNA

April 1, 2009

While we are on the subject…

…ran across this today. It’s a good one! Check it out.

The Quantum Surrender of Science

Science, a once-paralyzed minority of yesterday’s evangelical world, has long last come to the pinnacle of its predecessor. Scientists, now modern day vicars of faith, don fact as surrogates for dogma in their indoctrination of the ever impressionable public mind. As if clergy of old, their methods of derivation remain sacrosanct outside of scientific circles, impervious to the same investigation they readily apply elsewhere. To question the possible defects of the system that produces the central truths by which we live is to question reality itself, for how well our world view has been prescribed by scholastic teachings of scientific convention. All of our lives we have been taught that the world is a predictable place, and where it is not, thereby a lack of information, and not science, exists. We have been told to hold our tongue and quietly shave with the Razor of Occam when faced with the complexities of the unknown. But, let us exhibit caution before we obediently lock ourselves in the edifice of science, for a house of verity built on a foundation of error is sure to fall. Truths, despite adherence to the rules from which they are erected, become little more than falsehoods under incomplete laws of construct. Heterodoxies Blog presents The Quantum Surrender of Science, a composition on the deconstruction of scientific axiom, which aims to usurp the primacy of science by means of its own dilation, as the progression of such institutions are to be understood as an evolution, and not as the doctrine of truth we have been made to believe.

The middle is the best part.

What is needed now is the persistent disposal of scientific models that are limited to reductionism, determinism and localism, to be replaced with new models that consider factors from both higher and lower hierarchical levels, as well as those that acknowledge the observer and the act of measurement itself on reality.

Models focused on the systems approach, understanding processes and their control mechanisms, will take us to an objective view of objects, a higher level of functionality.

But most of all, in our infinite trek for truth, our scientific models of tomorrow must not only remember to bring society and its educational establishments along for the ride, they must demand participation from the true unveilers of the infinite realities they seek to ascertain.

I agree, but can “science” really give up? They seem to be turning deeper into their contrived material fantasy world. Meanwhile, the pseudo scientists, new agers and witchdoctors are leaving them behind, ready to embrace Quantum Mechanics as evidence of the existence of a mystical realm. Unafraid to incorporate QM into their understanding and improve their performance in real life. Even if science gets their models right, it could be another century before they can put them to proper use. You and i can put this knowledge to use today.

Meditate on it.

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March 12, 2009

The Human Experiment

Filed under: Ch 10 Conclusion, Drafts — Tags: , , , — insomniac @ 9:30 am

From the beginning of this project i’ve tried to keep my quotes and explanations as simple as possible. I’ve quoted mostly from encyclopedias, dictionaries and wikies, sticking to popular concepts. I have been reluctant to quote from scientific sources directly for several reasons. For one, experience has taught me that it isn’t a good idea to quote people out of context. Many time i have marked an exciting quote, only to find later in reading the author that my interpretation of the quote was based on my own world view. It made sense to me in ways not intended by the author.

Lately however, i’ve come across several folks within the scientific community that are clearly working from a similar context. I think i can quote some of them without stirring up argument about what they meant to say.

In the book, “Programming the Universe”, MIT physicist Seth Lloyd says,

“The universe is a quantum computer whose computations are the movements of information that define the world we experience.”

Seth is one of the leading experts on quantum computing, actually having built one. I had never heard of him until a couple of weeks ago, but some of his stuff sounds like we could have collaborated. Not so, i assure you.

I interpret the above statement to mean the rules of quantum mechanics move the information we experience as consciousness. I don’t think i am stretching Seth’s intent.

In this same time frame i have discovered Nick Herbert, whose book, “Elemental Mind”, also sounds familiar. His take is that “mind” is a fundamental natural process like light or electricity.

There again, i am pleasantly surprised that the conclusions reached by these experts in physics are so close to my own. Mind, conscious and unconscious, are fundamental functions of information processing that control and manage activity in biological systems.

All Knowing Universe

The System is intelligent. It isn’t just clever, but truly all knowing. The Universe is the memory of everything that has ever happened. It knows everything about itself, but still has to maintain homeostasis. Like any complex adaptive system, variables must be monitored, goals identified, strategies devised and implemented to maintain its level of success.

Living systems grow, reproduce and disperse into the environment in an experimental mode, (sandbox), constantly testing new configurations against the results of all other experiments. The system learns to adapt to its own adaptations.

Observation, Planning and Action

The physical Universe is the memory of the process of It monitoring Itself. The process is observation, planning and action.

Just like ants and bees, we build to the patterns in our heads. We build objects out of matter, adding our spiritual metaphors to Universal memory. These objects represent our contribution to what the System knows about itself. We human beings are experiments that devise and carry out experiments on our own.

As we repeat the cycle of observation, planning and action, we learn. LifeOS is always observing, planning and acting; growing, reproducing and dispersing; creating, testing and choosing; in short, learning. The obsessions that drive our science and industry are not unique to human beings, but expressions of the fundamental intent inherent in Life itself.

Protected Area

So we humans have been put to the test. We have been given experimental capabilities. We are operating in our own sandbox. We have been given all the resources we need to be successful. The worst we can do is fail. It is up to us.

March 11, 2009

Conceptual Sandbox

There is another information processing concept that is used extensively in biological systems. It is a protected area called a sandbox.

Sandbox: A protected, limited environment where applications (e.g. Java programs downloaded from the Internet) are allowed to “play” without risking damage to the rest of the system.
–From computer-dictionary-online.org.

Virtual Machine

This limited environment has available all of the important resources the untested code needs to function, but is confined to a virtual machine where it can’t interact with the “real” operating system. This isolation makes for a safe place to experiment with new code. Part of what makes it work is the relative innocence of such an area. The coded elements within the sandbox are “unaware” that they are part of a larger system and operate as if they were an isolated entity.

As you can see, software development depends on this concept at all levels. In this conceptual environment, code can be tested and refined, errors, viruses and misconceptions can be identified and corrected, bold new ideas can be entertained without risk to established procedures.

Protected Areas

Natural systems, both biological and otherwise, make extensive use of this concept. The planet Earth is a good local example. Planets, solar systems and galaxies are isolated environments that certainly fit the conceptual model. Australia and the Galapagos Islands are also examples of protected and limited environments where new models can be tested.

From an evolutionary standpoint, a species serves the same function. Each individual agent the system produces operates in its own sandbox. An agent is furnished with its own operating system, its own algorithms and the ability to choose among them or make up new ones. Just as in its computer counterpart, the agent is unaware that it is part of the larger system and acts on its own, interacting with its own perceived environment. If this experimental agent is successful and survives to reproduce, the code passes the test and continues to contribute to the whole. If this version fails to reproduce, the code is rejected, and no damage is done to the system.

Nested Sandboxes

So, we can look at the universe as a system of nested sandboxes. In this view, every living thing can be seen as an experiment in sustainability. Natural selection verifies the success of the test, incorporating the tested code into a new configuration that also will be tested. Meanwhile, all experiments are monitored and compared through their holographic entanglement.

March 9, 2009

Resolving Uncertainty

What have we discovered in this journey through the system of Life? We have traveled from the smallest particles in the cosmos, past all the energy, matter and information available to us, right up to the Whole Universe itself, looking for reality. We have discovered that the Universe is not really solid, but consists of energy interacting with itself. Energy is always in motion. According to our best understanding, energy is conserved, that is, energy isn’t created or destroyed, but is dynamic, always moving and changing. All of this dynamic action follows consistent pathways that show a set of system wide laws, rules or protocols.

Natural Laws

So, we have only two elements to consider really; energy and the laws it follows when it moves or changes. Whether we consider those laws to exist outside of energy itself, or are contained within it, they consist of pure information. Our material universe consists of energy, organized by information we call natural laws. This interaction produces change and movement. On the macro level, we can use these laws to predict exactly where objects will be anytime in the future. It appears that uncertainty is very low at this level, making the universe appear to be deterministic.

However, any flexibility to adapt to change has to be allowed for within the scope natural laws. It should be obvious that the laws obeyed by living systems cannot be deterministic, but must allow for adaptive options. The uncertainty of the future must be resolved into the relative certainty of the present. That can only be done by making choices.

Intelligent Choices

We know that, at least in our own case, this ability to choose between options is a function of our consciousness. Regardless of the complexity involved, to evaluate options and make a choice, requires at least a rudimentary consciousness. Although it is true that conditional responses can be represented in code without consciousness being present, as in a computer program, code writing is an abstract process that requires much more “intelligence” than it takes to make simple choices. The simplest explanation is that conscious action is taking place at the point of action.

Now, if we can accept the fact that choices can only be made by some sort of conscious action, it leads to the conclusion that, anytime or anywhere within the system that uncertainty is resolved, conscious action is taking place.

Navigating the Future

We know that at the level of human existence the future is uncertain. We can see the future coming at us and we have the ability to choose our most promising path through it. We count on our experience to give us an understanding of probabilities involved in choosing our path. If we look at other levels of existence around us we see that uncertainty gets resolved in much the same way. We see plants and animals adapting to their environment by choosing options. Animals routinely make choices for food, navigation and mates. Some plants track the sun across the sky rather than simply putting their solar collectors in the up position. Tracking the sun requires memory, a feedback loop and and some sort of decision making process. Even the smallest single cell creatures move and change following rules. In biological systems, it is experience that makes the rules.

Quantum Leap

Now let’s jump to the tiniest of particles and look at how they behave. Down at this level the rules are different. Down here we can’t pinpoint where things are; uncertainty is everywhere. Particles appear and disappear, wave functions collapse if you just look at them and nothing seems real. How can such an inconsistent and unreliable collection of energy packets produce the concise material universe we know and love? Although the laws of Quantum Mechanics seem vague, inconsistent with classic laws of physics and even downright strange, they have proven experimentally to be the most reliable of any natural laws discovered by science. So, how do we make sense out of this seeming paradox?

Holoverse

The holographic model erases the inconsistencies and gives us a better idea of how it works. The position of particles within the atom are holographically linked to the nested fields of the larger system in which they exist. These particles don’t represent their own position, but reflect the current dynamic state of the Whole. In other words, the wave function, (all of the information pertaining to the state of a particle), represents the state of the larger hologram. The apparent uncertainty at the subatomic level is a mirror of the dynamic probabilities of higher(nonlocal) levels.

In this view, the flow of the universe is constantly resolving the uncertainty of the future into the past. Matter is the memory of that process.

March 8, 2009

Systems Theory Revisited

Filed under: Ch 05 Cyber Systems, Drafts — Tags: , , , — insomniac @ 1:35 pm

This past few weeks has been a whirlwind of revisiting, rediscovering and rewriting, not without some rethinking, but always focusing on a final draft. The process has been educational, for sure. However, the rewrites are going on behind the scenes, in another world, so to speak, and won’t necessarily get updated in this blog. So here is a quick update for the section on Systems Theory.

Although systems theory may have seen little application to biology in the United States, on the international scene there has been a steadily growing interest.

“The International Society for the Systems Sciences (ISSS) is among the first and oldest organizations devoted to interdisciplinary inquiry into the nature of complex systems, and remains perhaps the most broadly inclusive. The Society was initially conceived in 1954 at the Stanford Center for Advanced Study in the Behavioral Sciences by Ludwig von Bertalanffy, Kenneth Boulding, Ralph Gerard, and Anatol Rapoport. In collaboration with James Grier Miller, it was formally established as an affiliate of the American Association for the Advancement of Science in 1956.”

International Society for the Systems Sciences
http://isss.org/world/

I have been surprised and pleased that the scientists in this organization have come to many of the same conclusions about biological systems that i have.

LIVING SYSTEMS THEORY

“By definition, living systems are open, self-organizing systems that have the special characteristics of life and interact with their environment. This takes place by means of information and material-energy exchanges.”

The Living Systems Theory of James Grier Miller is described as an open system characterized by information and material flows. The properties ( or behavior) of a system as a whole emerge out of the interaction of the components comprising the system.

In the conceptual system developed by Miller, living systems form eight levels of organization and complexity:

The principal components are cells, in simple, multi-cellular systems; organs, which are groups of cells; organisms (there are three kinds of organisms: fungi, plants and animals); groups, which contain two or more organisms and their relationships; organizations, which involve one of more groups with their own control systems for doing work; communities, including both individual persons and groups; societies, which are loose associations of communities; and supranational systems, organizations of societies.

Regardless of their complexity, they each depend upon the same essential twenty subsystems (or processes) to survive and to continue the propagation of their species or types beyond a single generation. “The twenty subsystems that process information or material-energy or both account for the survival of living systems, at any level.” “Living Systems Theory is a general theory about how all living systems “work,” about how they maintain themselves and how they develop and change…”

It is both encouraging that this branch of science is still alive after fifty years, and discouraging that few scientists are aware of the implications.

Why aren’t they teaching Living Systems Theory in public schools? Here is something they could teach right along beside random mutation driven evolution that doesn’t have anything to do with religion, but would ease the transition to a more holistic understanding of living systems.

June 25, 2008

Darwin’s Computer

Filed under: Drafts, Evolution — Tags: , , , , , , — insomniac @ 4:15 am

Just think how different the theory of evolution might be if Charles Darwin had used a computer. It’s not that he needed to crunch a lot of numbers to check out his theory, it is just that he was operating without the benefit of many basic concepts that the computer represents. For one, he had no concept of a code driven system. He had no idea that his theory of evolution depended on such a system to function. Nor did he have any concept of DNA, the heart of that system. If he had understood just those two concepts out of the many that have come to light since, his book Origin of the Species probably would have been very different.

If he, or any of those individuals who helped define the theory in it’s first one hundred years, had understood that biophotons are emitted by DNA in living cells, if they had been aware of Cleve Backster’s experiments with living cells and their ability to communicate over great distances, or modern quantum physics, or holistic/holographic principles, or Gaia, or information theory, our present version theory of evolution might be entirely different.

The Digital Revolution

You know how it works; once a document has been converted to a string of code(digitized), the code can be modified, resulting in corresponding changes in future copies of that document. You use your computer to read or modify the document by changing the code. That is great for documents, but it was found that the same principle applied to any manufactured object. In an assembly line run by digital computers, changes in code can be reflected in immediate changes in the manufactured product. That’s a big deal.

Furthermore, the digitized virtual object can be tested in a virtual environment and improved without having to build one. Many other things can be done with this virtual object, like ordering materials and designing the packaging or calculating shipping weight/cost, without ever having a real object. Computers have revolutionized the manufacturing process. It is easy to take that for granted these days, but just a few years ago, people used their brains to do the very same thing. Yes, believe it or not, people would build virtual models in their heads and test them to see how they would do.

Besides just the discovery of the DNA molecule itself, the big deal was to realize that DNA also functions like a string of code. Changes in the DNA result in corresponding changes in the bio-manufactured product.

Code Driven System

Once you understand the basics of a code driven system, it is obvious that random mutation cannot be the source of change in biological organisms. That is, the changing of one bit by random mutation compromises the code, maybe even breaks it. Coherent change can only occur when a viable string of code is added or replaced. It is like in a written language, the changing of a letter here and there doesn’t usually affect the meaning except in cases where changing one letter actually changes one word into another. Even then, the new word must fit into the old context to work. So these single errors are easily spotted and corrected and the overall meaning remains intact. In order to significantly change the meaning of a passage, many letters and words must be changed or rearranged. It is the same with DNA code; random mutation breaks the code, meaningful change happens when larger strings of code are added or replaced.

It has already been established that genetic material is fairly mobile in the environment. Fragments of genetic code are carried around by viruses and such. So we have a proven mechanism that can easily replace random mutation as the source of change in evolution. Well, it’s not easy, is it?.

This is not a new theory. The old theory is known as panspermia. A more modern version, Cosmic Ancestry contends that spore born organisms carry bits of DNA that are incorporated into the DNA of other species to produce change. Dr. Fred Hoyle has been telling us for years that spores are well adapted to travel in space. So, DNA arriving from space and being incorporated into terrestrial DNA could explain a lot of things that don’t presently make a lot of sense.

This would account for the some of the strange findings of the Human Genome Project like finding identical strings of DNA in humans and coral, for example. If the DNA evolves in place, identical strings of code in these two totally different animals doesn’t seem very likely. But it makes sense if genetic material moves around like packets in a network. Time to update our thinking in this area.

What’s holding up the paradigm shift? Once one starts down this path, it becomes a slippery slope that threatens to collapse the whole of western science. Recent discoveries in bio-electrics and quantum physics back up what the mystics, seers and sages(not to mention witchdoctors, hippies and new age cult leaders) have said all along… that the universe we live in is intelligent, willful and has a memory, as do all of the creatures that inhabit it with us.

If Darwin had used a computer, we could just go back into his original document and update the parts that need it and we would all have the new paradigm on our desktop. But alas, our document handling is still evolving.

cheers,
jim

June 7, 2008

How can it be both?

Filed under: An Introduction, Drafts — Tags: , , , , , , , — insomniac @ 3:56 am

When i came back online i considered changing my handle from insomniac, ‘cuz it no longer seemed to fit. Since retirement, i’ve been sleeping straight through.

Well, here i am, three in the morning, pondering at the keyboard, just like old times.

How can it be? How can the Universe be both material and ethereal at the same time? This is a fundamental question being asked over and over in blogs, on message boards, street corners and cafes. It is the single argument with so many different manifestations. Particle or wave, fact or fantasy, mind or matter, determinism or free will all stem from the same question. How can it be both?

Easy; it is all in how you look at it. The Universe consists of matter, energy and information. If you look at the matter by itself, it seems solid enough. If you look at energy by itself, the Universe looks chaotic, random and very hot or cold. If you look at the information by itself, the Universe becomes a phantom history of the doings of solid things amid chaos. Our Universe consists of all three. Considered together our Universe becomes less solid, less chaotic and more rational.

Is it solid or is it imaginary? Both! The Universe is solid, but dynamic, made out of energy and therefore not so solid over time. The interaction of matter and energy over time produce information in the form of an active memory. The Universe isn’t imaginary, but it has an active imagination.

You and i work with our own personal version of that universal user interface. The System lets you perceive your interface any way you see fit. It is done to you as you believe.

cheers,
jim

May 20, 2008

Shared Myths

Filed under: Drafts — Tags: , , , , , — insomniac @ 6:55 am

As you might know by now, i’m neither a scientist nor a theologian. Although i’ve studied both world views in some depth, i don’t think either has presented an acceptable model of reality. Both groups have fashioned their model of reality upon myths meant to subjugate human minds and bodies to their will.

Looking at human society as a cybernetic system, groups of people behave according to their beliefs. Beliefs are the protocols that set the parameters for human behavior. The beliefs fostered by both religion and science are what leaders use to influence the behavior of their followers. Those beliefs are taught to citizens by an elaborate system of churches, schools and peer guidance, that operates as if it were being directed by conspirators, or some other method of system-wide management. The rules that the individuals follow benefit the group that makes the rules. It doesn’t matter which way the information flows, there is a definite connection between micro and the macro. Just how that happens is not as important as the realization that such feedback loops exist.

The primary myth, perpetuated by both religion and science, is that the Universe is organized as a hierarchal pyramid structure with either a god or the human intellect at its peak and the environment just below the bottom. In this model, the information trickles down from the top.

So, please don’t put me in either camp. If you must locate me in relation to the debate between religion and science, place me firmly in the leftover territory; that of magic, the occult, shamanism and all the forces of Nature. Where i live, the information is supplied by the System, and the information travels in all directions. It loops back on itself in an endless flow, circulating information just as surely as it circulates energy and building material in any living organism. Denial of the information flow present in biological systems severely hampers one’s access to that information.

August 20, 2007

All Natural

Filed under: Drafts — insomniac @ 8:27 am

All natural

Manmade equals natural just as surely as a bird’s nest is a natural product.
So, the term “manmade”, may denote a certain class of artifacts that were fashioned by human beings, but those artifacts are as natural as can be.

The term “artificial intelligence”, is a misnomer in that intelligence is a concept that transcends the medium that is being used to express “intelligent principles”. “Artificial” describes a class of intelligence machines built by human beings that store intelligent principles for later application. However, creations of human beings are all natural, which includes our worldwide computer networks. The internet is as natural as a bird’s nest.

Cheers,

 jim

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