DNA Operating Sytem BIOS

In order to make a complete DNA operating system it is most efficient to use a structure that is an interpreted build language with primitives. By using the interpreter as its own compiler the process progresses logically and corresponds much better with the optimized capabilities of the machine. When asking for a list insert, canned code can be used as long as the user applies the function by name and it avoids the use of library structure which can be cumbersome.

The machine code in this case is a string of DNA which is 'compiled' by the biological system. An example would be a function 'f' with a variable 'x'. This would encode the initiator for the function 'f' as it translates from DNA, to mRNA to Amino Acids. The object or variable is a string, as all things in the system. The function itself is a string and it might be defined as "(define (SearchDNA x) ("GCATGTACTGA" x) ) in a scheme like syntax.

A "TRUE" is the product of the search which promotes a DNA sequence that encode A or B which either activates by induction the TRUE path or the FALSE path.

The compiler can be of several constructions I have seen in the lab. There are some nanomachines that use template DNA bonding on shape and this is feasible, but I know someone who does both cloning and nanomachines for a National lab and their approach is much cleaner and more natural as it uses nano to instantiate DNA that ultimately does the work.

The key element is a DNA sequence that accepts input from an external system to extend its own DNA. The rest is a matter of understanding the parallel aspects and the "hardware" on which it is implemented. The wide range of hardware that Linux is implemented on is nothing to what exists in the world. Each cell type is its own platform and as such each system has a uniques infinite response to changes in is "microcode". Having done initial development for the first PCs and having designed microprocessors from scratch, it is a similar issue. In this case however the designs have already been instantiated as Proofs of Concept. It is simply a matter of altering their BIOS to act in a way that is a bit more effective for survival and utility.

The methods are well beyond parallel in their complexity. Parallel methods do not isolate well in the universe. Many factors influence the overall process, such as number of active sites, competition for base pairs, availability of ATP, transient pairing of similar promoters, kinetics, and a vast array of other complicating factors.

A system is established to mimic the behavior and thus continuously interpolate to the best model. Digital logic can't reach the level of granularity that corresponds to a physical system and so it serves as a general estimate of what methods might be applied, without testing in a physical framework.

It is only this infinite soft&hard-ware that can understand its own complexity. It can be vastly parallel and functions in certain aspects to compute at the lowest possible incremental state of the universe, which would correspond in type to a virtually infinite word width computer.

Cloning an organism with new and altered DNA is common place in many junior highs now.

People once rode horses, and they produce no Hydrofluoric Acid as a by product of their manufacture.

The first task is to assign meaningful mnemonics for the language. I feel that if I can establish a language that has two personalities that would be best. For instance I could write and compile the program as "concat string1 string2 at L" or I could use an more elegant sentence as "Add the sequence called string1 to the left end of the sequence called string2". I can use a pre compiler to convert forward and back to a more understandable code template.

The simplest system might be comparable to a Yeast hybrid that uses something like this to instantiate an IF THEN or non-inverting or inverting gate. I have done this in the lab with GAL and I am sure the implications were lost on my instructor ( In fact I am sure of that. Few polymaths exist in such complex fields. Many scientists cannot program or design hardware.) I was very happy to see that I could implement an inverting and gate in the model organism and that it bred true to be a rather large NAND gate array, but then we must start at microns to get at Angstroms. I took some liberties with the experiment to prove that it was in fact a functioning computer and though the cycle time is limited, it expands in three dimensions without manufacturing cost and functions in parallel at the atomic level. Joking: The manufacturing costs are the killer though and this is the great expense, you need sugar and that is regulated by the FDA as a toxic chemical.

The use of TAQ and restriction enzymes serve as a model of the process, but are cumbersome. The BPU ( Biological Processing Unit ) must have within its instruction set the tools to splice, insert, and remove. Many of the concepts of digital logic apply in some form or another. It is possible to have deadly embrace as easily in a DNA system as it is in a code Lock semaphore. In fact, deadly embrace is a necessary aspect of the effective living BPU.

So the primitives are:

  1. cut DNA @
  2. couple DNA all
  3. create DNA string
  4. delete DNA string
  5. insert DNA string @
  6. transcribe DNA @

It would seem that a very limited set of primitives would compose the OS core as the objects are themselves methods and functions. Every object in a cell system is also a method. The composite function is determined by the order of execution. The programmed cell would differ from a living cell in the fact that it would have the ability to mutate itself in a continual fashion. It might seem like a dangerous process, but life is not an easy thing to implement in dominance. The players in this game have been around for billions of years and they know tricks that we are likely never going to understand. I can see patterns in things which tell me that many persistent organisms will operate in ways that seem illogical in order to place themselves in a survivable niche in the grand billion year scheme of things.

The Frankenstein principle of pulling a brain from one organism and implanting it then shocking it to life is so naive. I am sure that throughout history people have said they are moments from total understanding and that is the arrogance of life speaking. I do remember in the 1960's when it was assumed that all disease would be cured by miracle drugs like penicillin.

Life is not fragile, it has survived ice ages, super volcanoes, asteroids, earthquakes, and even humanity.

Natural dangerous organisms have a place in life. The overall result of the process is an interaction that compounds infinity on a 1040 framework over 4 billion years. It is fantastically intricate and in its detail almost impossible to believe. A single celled protozoa is vastly more complex than the most advanced super computer.

Having studied medicine, pharmacology, microbiology and genetics I have been exposed to many facts. The common impression of what is taking place is way off the mark and I would hesitate to discuss some of what I know, because it would probably disturb many people. What is going on in biology is nothing like what people imagine and the very nature of life is different than many suspect. My opinion is that philosophy must come from an understanding of the universe.

I assume most people have an idealized view of their existence that is almost cartoonish in its simplicity. Complex multi-cellular life functions more like a complex universe than a being. Many people expound on philosophy and existentialism, but I would guess from my perspective that they are reasoning from limited information and inappropriately extrapolating based on principles which do not exist.

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