LifeOS: exploring the system that executes DNA

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.

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February 7, 2010

First Friday Fractals

Filed under: Fractals, Life OS News — Tags: , , — insomniac @ 8:31 am

Had the pleasure of attending the First Friday Fractal show at the Planetarium, at the NM Museum of Natural History and Science, in Albuquerque. Wow! Jonathon Wolfe puts on a fantastic show. I saw one of his presentation in a classroom setting. Although the logic was the same, the impact of flying thru fractals projected on the dome, is something else altogether. What a show! It got me thinking…

One of the amazing things about fractals is that they produce patterns that we can see in Nature. We can see that Nature is using a similar technique to produce patterns involving matter and energy. How does that happen? Does Nature have a formula written down somewhere? Let’s compare the two, looking for the common elements.

The computer generated fractal phenomenon is purely informational. A formula is processed, and the results reprocessed using the same formula. The repeating patterns are the result of processing information. There is no matter or energy represented, only pure information.

A computer is processing pure information, nothing but ones and zeros. In order to compare the two we can look at Natural process as also processing information. Instead of ones and zeros, the Natural system processes atoms and molecules. It manipulates them to produce its fractal patterns in real matter.

The point of LifeOS is that information processing is fundamental, to the interaction between matter and energy, as well as to life itself. Fractals show that, without a doubt, the model of life as an information process is valid. We can assume the rules that Nature follows to produce its fractals exist, somewhere. They are certainly not written down in a mathematical formula, but exist in some medium, that not only retains the same relationship between values as the formula, but adjusts variables and even formulas, to suit the situation.

As shown in the magnetic cactus experiment, it is the magnetic field that adjusts the appearance of spines in cacti. It is the magnetic field in the growing tip of the onion that plots its pattern for growth.

Although reductionists like to jump on fractals to point out how simple process, repeated over and over can produce complexity, the fact that these billions upon billions of simple steps are coordinated to produce a specific outcome, infers a higher control mechanism is at work.

Networks in complex systems grow in two ways… hierarchical and scale free. In biological systems, these two options are woven together into networks that display both characteristics. Organs develope elaborate internal networks that use both types to accomplish their role in a larger outcome. Organs are connected to their peers and the larger networks through external, primarily scale free, type links, but include hierarchical elements, as well.

The coordinating element on all of these interactions is electromagnetic energy, expressed through fields. It is these purely informational fields of energy, distinctly nonmaterial, that guide growth, whether it be in crystals, biological systems or galaxies.

http://fractalfoundation.org/fractal-shows/first-friday-fractals/

So, i guess this book isn’t finished, just yet.

cheers,
jim

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.”

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