LifeOS: exploring the system that executes DNA

March 6, 2011

First Podcast




Will there be more podcasts? Time will tell.

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September 17, 2010

So What?

This is a text version of the Flash Movie promoting my book.
LifeOS

All organisms alive today, plus the remains of all living things that have gone before, all the organic compounds, all fossils, all fossil fuels, all the biomass accumulated by this planet over billions of years, exists because information coded into DNA was accessed, read and acted upon by a cell. Before any one of those cells could grow, before any living tissue could be manufactured, before any polypeptide chains could be assembled, before anything could happen in ANY cell, DNA information had to be processed. Information processing is the very first act of Life.

“So what?” says the guy in the back. Good question.
What are we talking about… Information processing. The first info processor we think of is a computer. Our civilization is driven by computers processing information. What makes computers so powerful is that they represent a fundamental process. Everything we see in this physical Universe is the result of a process. So a computer can be programmed to mimic just about anything out there.
Information Processing Loop
A computer can do this because it processes ones and zeros, following the same basic steps as any process. It starts with input and processes that input into output. Our nervous system processes information from the environment and presents it’s output to us as consciousness. Both are information processing in action.

Okay, at the micro level, information processing is a pretty good model for how things work. When we take info processing to the macro level, we have billions of computers hooked together in a global network, each one cranking out billions of those process cycles every few seconds. Altogether they generate all of the content the internet is displaying right now, including this.

It has taken millions of pretty smart people several decades, to figure out how to build and maintain this incredibly complex network. In the process they have discovered a set of mathematical laws that govern the growth of networks in complex systems. They have found that these laws are the same regardless of scale or implementation.

That is, the rules are the same for computer networks, neural networks, cardiovascular systems, river systems, social networks, bureaucracies and just about anything that grows to move matter or information. All along Nature has been following the same fractal power laws that we have developed for the building of the internet.

So, the internet represents fundamental process, and a global interconnected system of processors, that mimic Natural systems. The language of information technologies provides a common vocabulary for discussing everything from Biological Systems and Evolution to Quantum Mechanics and Consciousness.

What we have here is a universal language that describes information processing and its networks in minute detail. This is the language of the 21st century, taught in schools all over the world. This is the language and model of process that we need to give us a common denominator for a unified theory of reality.

Once we start to look at biological systems as being information processors first, with protein production being secondary output, a very different picture emerges of their structure and organization. Come along with me while we explore this exciting territory.

LifeOS now available at Amazon.com

Free pdf download from Mama Yerba Publications

Get in on the discussion right here. Comments welcome!

July 7, 2010

LifeOS Published!

LifeOS
Hey, it’s true. Way back on March 6th i said that the publishing process had begun. Well, yesterday the printer shipped the first order. I am told that it might take 6 to 8 weeks for Amazon and the others to include it their catalogs, but they will.

Ann Lowe did a fine job on the cover and interior design. It was really exciting to hold the proof in my hand. Ahhh, but this is only a beginning… somebody has to buy it! One step at a time, jim. =-)

March 8, 2010

What is Consciousness?

What is consciousness? That which observes fields of information, matter and energy, and calls them reality. Need it be more complex than that? Fields of information, matter and energy comprise our environment. Our consciousness interprets the environment and acts within it. We watch.

If that isn’t enough of a definition for you, there are more involved version to be found almost everywhere you look. Everyone wants to take a shot at it; we all have one. There is Consciousness Online, Center for Consciousness Studies(U of A), as well as dozens of universities, new age retreats and thousands of blogs that tag themselves as relating to the subject. The variety of descriptions reflects the difficulty of the enterprise. Every individual is describing a unique view of “reality”, that has been learned within a unique context. Every field of study has its own unique viewpoint, (piece of the elephant) that influences their observations. On top of that, each discipline develops a unique jargon to describe what they “see”. I call it the Tower of Babel approach. The more you read, the worse it gets; agreement on this subject is rare.

What this discussion really needs is a common denominator. The inquiry needs to be scaled to a level of functionality, where language and terminology can be used in common.

Rather than looking at consciousness from our human perspective, we need to look at how reality and consciousness relate to biological systems in general. Rather than concentrating on the complex internal details, let’s look at how the process functions at this higher level. At this level, the functionality of mobile species is simple: they move, eat, grow, expel waste and reproduce. We don’t care what goes on in their heads, just that they function within the environmental system they inhabit. However, we can note that the ability of an agent to be aware of its surroundings, is essential to three out the five functions. In its simplest form, awareness involves the processing of information. Here we can find some common ground.

The studies of complex systems, quantum mechanics, cybernetics, cellular biology, single celled organisms, chaos theory, fractals, holography, bioelectrics and information technologies share some common conceptual underpinnings. They are all explorations into information processing. There are many rules and laws that are consistent across these fields of study. They share common formulae for the construction of networks, for example.

The language developed by information technologies is known and understood across all languages, national and cultural boundaries. It was developed with functionality as it’s goal, and information processing and distribution it’s primary functions. Biological systems exhibit nearly identical patterns of functionality.

We find the same patterns of process in action in cells where DNA finds, copies and transfers genetic information. The universal rules and laws governing robust digital networks, outlined by Information Technologies offers the foundation for a common language to discuss consciousness, biological life and the material universe, as well.

The second common denominator is that consciousness, cellular activity, quantum mechanics, atomic structure are characterized by fields. Just as our consciousness is the result of waves of firing neurons(fields), matter is the result of waves of atomic particles interacting through fields of force(energy).

From plasma experiments, to growing tips of plants, to firing neurons, it is fields, processing information, that guide interactions. Consciousness is just such a field, processing input and directing actions. Looking at it in this light, all biological processes cycle through a phase of pure information, on the way to a phase of pure matter. Once it is seen as a fundamental function of biological systems, rather than an exclusive attribute of human evolution, consciousness reveals itself.

cheers,
jim

February 19, 2010

Directed Mutation

“In 1988, geneticist John Cairns published what has since become a revolutionary paper entitled On the Origin Of Mutants (Nature 335:142, 1988). Cairns recognized that gene mutations were not solely the result of random chemical events as is currently perceived. Cairns placed bacteria, possessing a defective gene for the enzyme lactase, in Petri dishes that contained only lactose as a food source. The mutant bacteria were not able to metabolize the substrate. After a short period, the stressed, non-replicating bacteria began to thrive and proliferate. Upon examination, it was found that the bacteria specifically mutated the unresponsive lactase gene and repaired its function. Cairn’s research revealed that, in response to environmental stresses, organisms can actively induce genetic mutations in selected genes in an effort to survive. These mutations would represent mechanical “adaptations” that are induced by the organism’s response to life experiences.”

The video is here:
Adaptive Mutation

Immediately, the bureaucracy of science went to work. Cairns called it, Directed Mutation. That terminology was unacceptable to his peers. A paper to put this new information in proper scientific context was soon published.

Copyright 1998 by the Genetics Society of America
Adaptive Mutation: Has the Unicorn Landed?
Patricia L. Foster

In the second paragraph…

“Early in the project, we established that the mutational process was not “directed” toward specific targets (i.e., there was no reverse information flow) (Foster and Cairns 1992), and we renamed the phenomenon “adaptive mutation” (Foster 1993). We then pursued the alternative hypothesis that during selection a random mutational process affecting the whole genome might occur; the process would be adaptive if the variants (or the cells bearing them) were transient unless or until a variant arose that allowed the cell to grow (Cairns et al. 1988; Stahl 1988; Boe 1990; Hall 1990). Although less efficient than a directed mechanism, “trial and error” would have equivalent implications. With such a mechanism, a population could increase its genetic variability under stress yet maintain its genes more or less intact.”

So, right from the start they had adopted Crick’s “Central Dogma”, as a given: “there was no reverse information flow”. The truth is, they never even looked at the flow of information. Just as in the laws of thermodynamics, where energy doesn’t come out of nowhere, neither does information. Information is the result of process, and follows pathways that ALWAYS loop back to their source.

Anyway, “We then pursued the alternative hypothesis…” This is how they do it in science. They fudge their results with the unlimited power of “jargonese”. But it is language that gives them away. Words like, selection and adaptation infer that choices are made. In fact, the details of these experiments show that information is being processed. Information processes(like choosing) are firmly in the domain of intelligence.

Mutations, changes in DNA sequences, follow the same pattern of information processing as would a team of scientists trying to solve the same problem. The inability to metabolize lactose would be met by several proposed solutions, with only the best one, selected. In it’s simplest form, analyzing a situation, proposing options and processing one to a successful outcome, is very intelligent action. To ignore that possibility because of preconceived bias, is not very smart.

Directed or adaptive, doesn’t make much difference; a mutation that successfully accomplished a targeted goal, certainly cannot be seen as a random process. There was no cell division, no opportunity for random errors to participate, no natural selection at play, only reorganization of process in order to adapt to an environmental situation. The attempt to “explain away” the implications with mountains of jargonese shows that they just don’t get it. They assume from the start that, “…there was no reverse information flow”, just as did Crick and Watson. This is where the information processing model exposes the blind spot of central dogma. There is no reverse flow of information, but it loops back through the system, where choices are made about what information completes the circuit. It walks and quacks like a very smart duck.

February 2, 2010

Science & Spirituality

perspectives
by Romik Kimor (videos)
17:28
Science & Spirituality – The Essence of Life from Two Perspectives: Dr. Stuart Kauffman & Dr. Fritz-Albert Popp

Quantum fields, biophotons as information that controls cellular process… good stuff!
This one requires a plugin.
This is on my facebook page.

Dr. Fritz-Albert Popp:

“Biological Systems are governed by the special
interaction of a coherent electromagnetic field (biophotons) and biological
matter. There is a permanent feedback coupling between field and matter
in a way that the field directs the location and activity of matter,
while matter provides the boundary conditions of the field. Since
the field is almost fully coherent, the interference patterns of the
field contain the necessary information about the regulatory function.”

January 24, 2009

Ultimate Undo

Filed under: Ch 09 User Interface — Tags: , , , , — insomniac @ 4:59 pm

In a dynamic environment the individual must also be able to learn quickly. From a species standpoint, attempted changes in the structure to meet environmental variation must be temporary. The species has to test new features thoroughly before they become permanent. What we would like is a limitless “undo” option. That’s easy when your data is managed properly.

Rewrite Old Files

Imagine you have a document you are writing in your computer. In the old days of word processing, each time you made a change to your document and saved it, the document was re-written. The code was changed to reflect your changes and a new copy of the total string of code representing your document replaced the old one.

In the old days we used different file names so we could preserve copies of major stages of development of the piece, in case an approach wasn’t working we wanted to go back to an earlier version. Still, each document was saved as a complete and separate file.

Software Evolution

That works OK, but word processing has evolved. There are more efficient and flexible ways to handle documents, that result in handy features like, “undo”. That is the ability to reverse earlier decisions. For the ultimate undo feature, we want to be able to back up through all the steps we have taken to create this document, from publication, back to the first sentence. That would be a lot of documents if you saved each step as a complete and separate file. However, if you save each revision of the original in a database, with references to position in the document and keep track of all changes, you can recreate any former version and you don’t need a lot of separate files to do it.

When you export a document, the word processing software assembles a finished version from the elements stored in the database, according to your latest changes.

Dynamic Memory

The concept we are working with here is that of memory as a cumulative recording rather than a static picture. We are talking about a dynamic memory that records changes as they occur.

DNA works like that. It isn’t just a static record of a particular physical structure, but a dynamic physical reality that is the memory of the processes and changes made to produce it. It is one of the indications that sophisticated information processing techniques are indeed operational in biological systems. The stability and robustness evidenced by billions of years of successful modification of DNA code, cannot be attributed to random activity of any kind.

Even though DNA is quite stable, its product is capable of modifying future DNA and thus de-stabilizing the entire system. However, DNA is always dynamic, never repeating itself exactly, always presenting a new design, modified for testing in real life. If successful, this new design can be compared to past designs in real time. What they call natural selection, is the final test for modified DNA. If the agent can reproduce successfully within its time limit, the improvements are incorporated into the design. If not, the test fails and the experiment is terminated. Natural selection causes the code to automatically revert to the last successful version. The ultimate undo.

October 25, 2008

Instinct, Learning and Adaptation

Instinct

“Learning is often thought of as the alternative to instinct, which is the information passed genetically from one generation to the next. Most of us think the ability to learn is the hallmark of intelligence. The difference between learning and instinct is said to distinguish human beings from “lower” animals such as insects. Introspection, that deceptively convincing authority, leads one to conclude that learning, unlike instinct, usually involves conscious decisions concerning when and what to learn.

“Work done in the past few decades has shown that such a sharp distinction between instinct and learning—and between the guiding forces underlying human and animal behavior—cannot be made. For example, it has been found that many insects are prodigious learners. Conversely, we now know that the process of learning in higher animals, as well as in insects, is often innately guided, that is, guided by information inherent in the genetic makeup of the animal. In other words, the process of learning itself is often controlled by instinct.”

Source: Gould, James L. and Peter Marler. Learning by instinct. Scientific American, January 1987. Reprinted in William S.-Y. Wang, ed.. 1991. The emergence of language. Development and evolution. New York: Freeman. 88–103.

Hard Wired?

What we have here is a learning/memory process that is shared by all biological systems. Nothing is really “hard wired” in biological systems. Even DNA is a pattern for growth and not a firm design. Even after DNA is expanded during cellular growth into a “final” adult design stage, cells grow and adapt to changing conditions. Hard wired is a term from computers that really doesn’t apply to biological systems, unless maybe that “learning” itself, is hard wired into all living systems.

Learning

Learning is a process that functions at all levels of biological systems. Looking at Life as an information processing system, reveals learning as a primary function of the system. DNA is the system wide knowledge base, stored in such a way to guarantee maximum stability and robustness. Every piece of code has a built in sundown clause. It is constantly being replaced with new code that has been thoroughly tested under real life conditions.

The life cycle of all living things is a two part process that simultaneously tests its DNA in the real world and learns about how the local environment is changing. Successful species continue to build on the knowledge base, adding and adapting to their experience.

The best designer in the world would not be able to design a mobile agent that could function successfully in a new environment without some knowledge of what that required. The system that designs agents must work from inside with intimate knowledge of the outside. The outside is constantly changing, so the inside must adapt.

Design Team

Even though the design team doesn’t have to redesign the whole agent every time, it needs to be able to set the appropriate control switches, like environmental triggers for imprinting and such. Each species has a set of specific triggers it expects from the environment in order to initiate specific learning patterns. Even though many systems and subsystems arrive fully functional regardless of the species, like basic metabolism, control and sensory systems, they still must adapt to resource availability during their development. They also grow and reinforce what is successful in real life tests. The design team will need to know the available food sources, their nutritional values and such, before they can set the necessary triggers.

Of course, there is no design team as such. I use the term to personify an observed function, for ease of discussion. It is a very handy tool, if the imagination is flexible enough not to get caught up in the analogy.

Whether the process is driven by dumb luck or an intelligence of unknown origin, the results are some very fine subsystems, of which the human animal is one. We seem to be very smart, however, our very best design teams produce nothing, but crude examples showing only primitive engineering savvy, when compared to the simplest life forms. Flatworms are primitive according to evolutionary standards, yet their design is extremely efficient, even elegant. From a system viewpoint, the flatworm design, represented by its DNA, is extremely robust, stable and well dispersed in the environment. It has been a very successful design. It is part of our exploration to identify the design process, wherever we find it.

Meeting Expectations

In building the LifeOS model, i was satisfied to have a system that would monitor reality and project solutions to problems, but idea that the system is constantly projecting an intended path is much more “intelligent”. Rather than have to identify “problems”, which could be a challenge, the system attempts to maintain a status quo. It treats any deviation as suspect. Seems to me that shows that the system is dealing pro-actively with the future.

In our culture, most people simply react to what comes their way. Our most intelligent citizens are people who don’t wait to simply react to events, but take control of their own future. These people set goals and work to reach them. Biological systems in general, are not just responding as would a person of average intelligence, but in the manner of one of superior intelligence; not by simply reacting, but by forming expectations(hypotheses) and testing them in the real world. This intelligent action is going on at the cellular level.

This is not in a long drawn out process, but a rapid firing cycle of cellular metabolism. With every cycle, the present input is compared to predictions. This process becomes a flowing wave of expectations, met or not, evaluated by waves of dopamine.

Animal Behavior

Back in Free Will i described the behavior of critters like cats and that bossy fly that quit playing by my rules. This is the same pattern of behavior that we find in dopamine neurons. These neurons are firing a steady stream of expectations that cause no reaction when they are met. Any deviation causes immediate adjustment to expectations. This stream by a single neuron becomes a wave when all the neurons are firing. This wave is constantly being compared to the waves of the past.

When an agent meets a new object in the environment, these neurons fire away, sending a flood of dopamine carrying info about the mystery object. It appears that the dopamine acts like a reward for the agent, making the exploration of new objects, “feel good”. It isn’t a simple on/off reward, but contains levels of description, evaluation and judgment. It is like emotion, with a wide range of feelings about the object. The simple act of observation begins an elaborate process of carving away the mystery to reveal the reality of the novel object or event.

When the new object is “figured out”, the neurons quit firing, the dopamine stops flowing, and interest in the object fades. Novelty and boredom controlled by the flow of dopamine. When a kitten is learning a new game, the dopamine is flowing. Once they learn the game, they lose interest. Back in Free Will, i attributed that behavior to the ego. The kitten and the fly just wanted to have their way. They just like to “boss us around”. From this new information, i would say that the reason for that behavior was because they learned the trick and their neurons quit firing. The dopamine rewards them for learning new tricks. Well, human beings are the bossiest of all, and our ego seems to be fueled by the same kind of neurons.

So, who gets bored? Who gets the reward that dopamine provides? Who is giving out this reward? When the fly or kitten turns its back on me and refuses to acknowledge my play cues, the animal is communicating to me that they are no longer getting the internal reward they need to stay interested. Who is initiating that communication? I still say, even the smallest creature has an ego, a sense of self that relates to its environment with intent, expectations and strategies.

Adaptation Happens

From a system viewpoint, adaptation must be a sought after goal of some protocol or other. Adaptation is accomplished by learning at all levels of biological systems. Adaptation is a fundamental attribute of Life, part of the protocols of its operating system.

June 5, 2008

Platform Limitations

Filed under: Ch 07 Biological Holography — Tags: , , , , , — insomniac @ 6:24 am

So far we have been talking mostly about the structure and operation of our inanimate material universe. This is the information processing platform upon which LifeOS is based.

In computer science it is important to remember that no program, algorithm, or process can perform any action that is not supported by the underlying platform. It is the underlying platform that does the actual work, it is only instructed by the higher level systems. The same is true in LifeOS, in that the system can only accomplish what is doable by the underlying platform of electro/chemical reactions available; i.e., Natural Laws.

The platform for life is matter. Matter is composed of light organized by the laws of atomic structure. That structure is the information that defines the difference between light and matter. In other words, just as DNA is information before it is tissue, the Universe of energy and matter that supports our biological system is also information first, before it is matter.

One of the most important principles in the LifeOS model is coherence between entangled/synchronized objects This fundamental electromagnetic principle has been proven to operate at the atomic level. When dynamic objects combine to produce a coherent electromagnetic field, we have a holographic memory system. This same principle has also been found to be operational in biological systems.

DNA powered Life acts like a higher level language, using the simple processes of the underlying platform in combinations that produce more complex capabilities. No higher level language can ever accomplish any task that is not within the capacity of the underlying platform. However, the higher level of organization makes possible tasks that the underlying platform cannot do alone.

The Platform includes a built in holographic memory system, universal addressing of objects and the objects themselves. The universal addressing system is holographic, so the address is a signal that includes all information regarding the object as its wavefunction. DNA amplifies and organizes this information to produce living tissue.

September 11, 2007

Biological Operating System

Filed under: An Introduction — Tags: , , , , , — insomniac @ 8:47 am

All creatures alive today, plus the remains of all living things that have gone before, all the organic compounds, all fossils, all fossil fuels, all the biomass accumulated by this planet over billions of years, exists because, information coded into DNA was accessed, read and acted upon by a cell. Before any one of those cells could grow, before any living tissue could be manufactured, before any polypeptide chains could be assembled, before anything could happen in ANY cell, DNA information had to be processed. Information processing is the very first act of Life.

Why is this an important distinction? Because information processing involves a set of concepts that are independent of the processing method being used. For one, there must exist a consistent set of rules or protocols that govern information processing within the system. This is called an operating system, or OS.

All living organisms follow the same rules for accessing and reading DNA code. These universal rules infer the existence of a biological operating system. I call it LifeOS.

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