In Circuit Emulator ICE for BIO -not- BIOS

In computers when they were first developed, the really effective tool besides an oscilloscope and multiple signal analyzer was the ICE machine. In biological terms it would be an IVE, which could be an In Vivo or Vitro Emulator. The principle is the same. In the case of cellular mechanics it would be the ability to single step the process by applying a clock of sorts. In this case it could be the depletion of ATP or another energy chemical that corresponds to the clocking energy for the process. It is also necessary to identify the state of the machine before and after the transition step or what serves as an instruction. I have a microscope which can identify molecules in a living system though it does have speed limitations for direct viewing. It would have to be configured through a high speed optical interface that could be viewed in a human time frame.

When designing a processor or a motherboard chip and even for analysis of microcode and BIOS it was critical to have the tools to observe the conditions and the effect each change had on the system to identify which effects were dependent. In the case of biological organisms the design is already completed by random evolution. It is necessary to retrofit design tools to enhance the design in any significant way.

Other tools that need to be completed are the compiler and what would be similar to SPICE for the interaction of protein, chemical and DNA pathways. The compiler would be critical for some techniques that I would like to implement as variations on the sequence. It is reasonable to assume that an organism can be devised which is completely resistant to disease. Its existence would have an effect on the biosphere in unpredictable ways. It could allow temporary blooms of super bacteria that would out pace their rivals by vast scales as would a complex multicellular organism which was not hampered by risk of disease.

Many great experiments have been devised to deduce the mechanisms of things like Ubiquitin and CDC2 as well as many other sequences. It is an impressive achievement considering the complexity. It is merely foundational and the rate of discovery must be many magnitudes higher in order to have a reasonable model in some sensible time frame. Like the advances in DNA analysis that have gone from decades to days, the process analysis must go from decades to minutes to achieve a complete interactive understanding. Sequencing is one of the tools and I can remember typing hexadecimal code into a UV erasable prom and compiling on a piece of paper. It isn't the best way to get anything really elegant done, but it did serve to advance the science. Computers and biology are very different subjects and though there are parallels they do not have the same impact when designed and implemented. Synthia has been created and I would say that this is a logical milestone in the philosophical base of understanding. The mystical impression that persists in the nature of being is certainly common place and it does imply that many people would be confused by some aspects of biology as it relates to things as simple as identity or continuance. It doesn't help when obviously incorrect arguments are applied commonly as if they were perfect facts.

ADDED: It occurred to me that this could be done in a sloppy way without a direct living microscope for a particular single celled organism if a specific sequence of events was to be modeled in detail if it was desired to know the precise chain of events in atomic detail. If cells arrested in a state and aligned in a tube were given a diffusion gradient of chemical or other control could killed and placed in order under an electron microscope like frames of a movie, but that seems awfully messy and time consuming as well as subject to interpretation.

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