Solved game of chemistry

A lot of areas are improving as I develop techniques to deal with science using my new tools. The infinite dimensions math is working fine, but needs some extensions. It does seem that chemistry is a lot like checkers and I have been reprogramming a checkers AI recently for experience and to get a feel for making a tool that models a chemical process.

What makes it possible is a certainty interface to bonding. By abstracting the physics of the interaction of atoms it is possible to play the combinations as moves. The real process is of course infinite in variation, but the chemical process has nodes which are present at each temperature.

I have two advantages, the ability to watch molecules interact, and the equation which defines the interaction between nucleus and electron. I have not devised a method to view the action of the electrons as they form bonds, but that would be a nice addition. I have a general idea of how that can be done, but it may be some time before I can make a prototype.

I remembered a design that I did in 2000 and it seems that I forget things that people don't duplicate. It is possible to make a cheap solar energy to electricity device. When I say cheap, I mean something like 10$ construction cost for a 10' × 10' panel. It converts using a process that does not require any specialty material and is simply a mechanical system. I discovered it as an extension of some toys that Volta, Tesla or somebody made. I am surprised that has not been duplicated by some other inventor.

( Not ( Accepting ( Infinity - x ) ( AI ) ) )

In the course at the link from Berkeley computer science about scheme, it is not as elegant as other courses in Lisp like languages ( most I have seen at MIT and Stanford ), but I feel it gets to the heart of the matter and I will attempt to dig deep and find reason here.

A language such as this defines functions which have data. Essentially it is f(x), where x is anything and f is a method. I could implement this as push x, call f, and that would be it. I can interpret the language any way I want. I can parse from "(" to ")" and select element 1 as function and then push push the rest. I compare syntax and then generate a function call corresponding to my interpretation of syntax. At its most basic level it is an operation on registers when dealing with CPU functions and I could assign opcode xx to be "mov" or "add" or "xor" or even "doodoo" if I wanted. The mnemonics and symbolism are unimportant.

If you start with infinites and then focus on partial infinites then you have a system of math and logic which is provable and complete. A person can device any number of circularly perfect systems and religion is one of those. I can start by asking you to assume one fact and then based on an assumption devise a complete system. That is an unfounded logic system and the system of math is an unfounded system. I am asked to assume 1 (one) and I cannot accept that, as odd as that seems.

The proof of pudding is in eating and the proof of a proper system is in its foundation in the universe. In the biological system it is a complex of infinities and each part affects every other part. I could be true that the structure which defines the hand could influence the nature of the brain. It is a system without limit and it is true that seemingly unrelated elements of a person's physical whole influence certain "metaphysical" aspects. A dog may not bark by design, but by his paws.

I am sure that is as clear as mud, but I hope to relate some example methods and systems that make the concept clearer.

Debian has a package for scheme called "mit-scheme" and it executes at command line with the command `scheme`. I suppose that the failure to use arrow keys is some compatibility issue and I can live with that.

Java chemistry

Discovered this chemistry resource with Java applets.There is so much information on the web that it makes education easy for a polymath. Chemical kinetic is an area of interest and I hope to extend this to interface with my bioinformatics tools.

Also this YouTube video from Google is way funny and extremely informative for somebody who wants to consider what does the this.java.code really do and why doesn't it do what I expect?

I also watched a Google video from Douglas Hofstadter of GEB fame, about Kurzwell and singularity. He makes some valid points and in my estimation, they are both wrong. They approach the same concept with different perspective, but when these things unfold, they present "things" which have never been observed before and as a result cannot be discussed as they never existed before they "emerged". It becomes an issue of predicting the future and that is not possible. So my opinion is that they look at what could be , consider what it means , and assume that is the end of the story. That is the problem, it is an unfolding of something that never becomes completely unfolded, it is the unknown and as such it may look like what they predict at some point in time, but it reveals new possibilities and new problems. The answer is that there is no final answer. Even in find bugs.

I see many things that could be and they can't all coexist. Things and methods become dominant or fade when new methods appear. A liquid "Terminator" might be the idea of the ultimate terminator, but it is just a passing fanciful concept of that which could be if the story ended there. I want to see a cage match between "Body Snatchers", "Wolverine", "Firestarter", "Carrie", "Scrooge McDuck", "Frankenstein", "Shirley Temple", "Genghis Khan", "The Godfather", "The Borg", "Buffy the Vampire Slayer", "Terminator and T2", "McGuyver", "KGB", "The Q Continuum", "Alien", "Dr Who", "Teenage Mutant Ninja Turtles", "Predator", "Superman", "Godzilla", "Tyrannosaurus Rex", "Harry Potter", "Dirty Harry", "The Goa'uld", "Babe Ruth", "USAF", "Mick Jagger" , "Samurai" and "The Puppet Masters".

Physical chemistry

The idea is not new and I have read several books at the university library on the physics of chemical bonding and I am not the only one who suspected that the description and application is poorly understood and badly implemented. Chemistry is a science that depends heavily on example and experimentation to identify process. No coherent theory of how bonds are made and broken has ever been devised which explains the overall action.

Theories describe the action in vague relationships that defy extrapolation. I have come to understand that underlying method of bonding. What takes places is obviously electrical in nature, but without an understanding of the nucleus, the nature of gravity and some understanding of higher dimensions it probably just looks like an amorphous complex of action without coherence. The idea that it can be completely characterized by probability mechanisms is absurd, but that it could be characterized without probabilistic elements is equally absurd.

For myself, I consider it no more complex than using a library function and understanding the interface well enough to apply that knowledge to achieve a specific result. For any specific application there are skills and information that need to be absorbed and understood. I have studied many things and the concept of n-Dimensional space as it applies to the understanding of electrical field action is certainly the most difficult to understand and apply. The mind is not well suited to grasp dimensional information beyond the 4 that it commonly manages.

Much like gravity, the bond between atoms and molecules is one of the ubiquitous elements of the universe and its understanding is key to any effective science. Certainly most if not all of chemistry is process based and this seems like an extension of alchemy as it originated. I kind of random application of experimentation until a specific condition produces a consistent usable result. Science in the gross aspects, much like melting metal and hoping the bonds form in the way you wish. The universe has no parallel to the construction of bonding by specific technique and this is because the condition which would allow this are not only improbable to occur naturally, but I assume virtually impossible. Like, on the order of 10^-billion that it would happen as a combination of events once for one single bond. It would require a random event that would rival the appearance of a 747 from thin air with a plane load of passengers.

As a random event it would be odd, as a mechanism it is quite simple. Okay, n-Space, electrical fields, probability relations, atomic scale observation, and nuclear physics, are probably not simple things to most, but I mean relatively simple if you grasp the basic concepts of the universe.

I did commercial chemistry when I was still in my teens and I can relate to not understanding what it all means. It is a confusing tangle of data that I saw as something like a Rubik's cube puzzle with 10 trillion faces and 100 dimensions of rotation. I can remember trying to understand it and sitting for days in a row studying the Handbook of Chemistry and Physics and attempting to get even a glimpse of a pattern. I can remember being physically sick as it was so complex and failing to understand things seriously disturbs me.

A lively puzzle

So now I am deep in The Heart of Darkness and I am modifying everything in concert as a grand symphony to make the puzzle pieces be Amino Acids and to use the equation of state of the universe to determine if the puzzle pieces fit and in what 3 dimensional structure. The game constructs a puzzle of (n) amino acids at random at first, but later uses the data base of known amino sequences and generates a 3 dimensional result and then generates "hints" about structure which would allow a person to solve the protein. It solves the protein structure itself and from this generates the hints with some sense, I hope.

I am keeping an eye out to make it extensible in dimensions and viewable in many different ways. I am also considering that I will implement it as WebGL with javascript and so all the essential interfaces will have two or more personalities to deal with assembly for WebGl or stand alone application. I will also include the option of using non-standard amino acids that arise on occasion. I hope to discover one of the issues that bothers me and that is branched chain proteins and also a specific sequence that I think exists and is not really life, but is somewhere above prion and well below Mitochondrion. It is a hypothetical structure that I devised as a result of analyzing some atomic interaction of various atomic soups. This means I need to incorporate other atoms beside CNSHO and other molecules in the interaction with the proteins and of course Phosphorous, H₂O , Fe, Ca, Na, and probably a few others too as time goes by.

I estimate it will require several months to get all this in a usable WebGL + javascript -and- local OpenGl + Xwindows form. By that time it will be spring and I also hope that WebGL will be usable by then as a standard in Firefox.

The entire assembly should provide the framework for a virtual world which is various types of cells or non-cells and allow travel inside the cell to view it as it operates in whatever time frame or scale is desired. Pretty much a virtual world, but with cell walls instead of concrete walls. I hope that it will explain some question that I have about PolyA tails, ubiquitin, walking molecules, other walking molecules, and ATP. Along with about a million other questions.

I hope the whole thing can be documented and written as meta-code generated from a single descriptor. It makes sense to me. Why send an image file when I can say "Use convert" or "Use ImageMagick" and "make image 512x512 color depth 8 with 6 dots on it evenly spaced in two columns as a png type image". Or I could just do that myself and send you 512x512x4 (4 million ) bytes in place of 40. It doesn't seem very efficient to me.

There is no need to have the kind of bandwidth that is generated by flash animations. Either give me the useless information or keep it to yourself, I don't care. They are sending millions of bytes of information in an attempt to influence my mind, that seems like trying to teleput into my head. If I wanted to teleput something into your head, and just did it without considering whether you wanted that in you head or not, wouldn't that be rude? The mind is something that can take that which is meta-physical and make it physical in the universe. That is a wonderful thing and I don't like people shoving random crap in my mind to make a buck.

Meta programming concepts and metaphysics

Is this meta-programming confusing or I am just slow?

$as_echo "cross-compiling" >&6; }  # FIXME

else
  cat >conftest.$ac_ext <<_ACEOF
/* confdefs.h.  */
_ACEOF
cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h.  */

#include <boost/thread/thread.hpp>

int
main ()
{
boost::defer_lock_t(); return 0;
  ;
  return 0;
}
_ACEOF

It is possible to create a structure of meta programming and code reuse that becomes self supporting. The concept of boost is to reuse code and the concept of analysis of structure is intermingled here as I use this code to generate structure in the form of `graphviz` and then `povray` which in turn uses `boost`, which is analyzed and interlinked. to display it. Here I attempt to use the output to the structural analysis of code to reuse the code in a meta way. The degree of recursion is very complex, but this is not anywhere near as complex as the recursion and interaction which exists within the genotype expression of even the simplest single celled organism.

There are some things in the universe like conservation of momentum which are absolute necessities for understanding the coherent ontology of the universe. Recursion is right up there along with some other characteristics which defy simple explanation, like tendencies to specific attractors.

I can read this shell code, but does it need to be this confusing in representation. I would guess that `python` could be used here with some advantages in readability. I will have to Google and see if there is an alternative to configure in python. It does exist, but there is a better way to represent all of these complex ontologies. I am sure that the term ontology does not even touch the complexity of what all this represents. The relationships extend and expand exponentially and infinitely. It is much like classifying a concept as "all that other stuff."

It does seem to be a bounded and solvable ontology. From my experience with the puzzle game I can establish certain dimensions to the problem and it is very much like self-replicating and self-assembling forms as they interact to produce a result which is recursive and coherent. That higher dimensional association is not clear when viewed from a normal perspective and yet is more observable from other angles in different dimensions of thought. It may reduce the factorial exclusions that are necessary to the point where I can get a single coherence. At that point, I will have a new amplifier which can expand till the next barrier of recursion. I am afraid I must add more complexity to reduce it. It very much reminds me of organic synthesis of using Diels-Alder reagent. It was not always obvious what would happen, but trying several alternate methods would yield the desired result. I never told my lab instructor that I may have used some "tricks" I learned early in life doing qualitative and quantitative analysis.

I see some interesting things just beyond the veil of this complexity and perhaps this is what always drives me on. It is that new understanding of something never seen before. Like a jewel of knowledge of incomprehensible worth.

Analogous Instrument(AI)

Below is an image that represents recursion of construction and destruction in the world of poly amino acids. This is the core of the operations of a cell. In the cell, the selection of a protein from a list is achieved through regulation of the DNA to mRNA conversion. The code generated modifies the universe and in the process produces itself as a final act. When I first modeled this process many years ago it gave me an interesting answer not pictured here ( because I am lazy and it is visually complex and difficult to represent in 2 dimensions ). When everybody has WebGL as a standard in their browser , I will be able to include 3 dimensional relationships as examples.

The statement that I wish to select one thing from a list and apply that thing is equivalent to writing a function that defines `int ArrayList[n];` `int thing;` `int select;` and then performs `select = rand()%n` `thing = ArrayList[select];` `return thing;`.

So, methods that a person might wish to program are items with a greater selection. This is where the computer shines. It has virtually perfect memory of what might be in a list of possible solutions. I can make IO functions that serve to allow the program to get information from audio, video , position information and other data that is "sense like" to define the choice matrix.

I think that I have the correct structure to allow this process to grow correctly and it is mainly the motive file, or the problem to be solved that will define what types of programs are generated and what data they are tested against. I can manipulate the process in any aspect, and I will likely place obscure methods in the method file to save some time and thrashing to determine the best algorithms for specific purposes in each context.

I will link an artificial imagination into the programs with generic interface. It is essentially an openGL interface that allows the construction of objects from lists of known objects to move, scale, shade, and rotate them. It incorporates a mechanism to take the frame buffer and compare it an image from any source. I already have many scripts that allow the conversion and scaling of images to the method that the program expects ( ImageMagick mostly ).

I feel there will be some interesting surprises to come from the generated code. If the method file is properly spec'd it would seem that it would always produce safe code. I will try and see what happens today. I plan to have a run which goes from description, to code generation from code design file , to compile ( chosen from language select ) , to splint, to gdb ( with XFakeKeys), to a virtual machine using Xfake also.

It seems that the program generator would be complex and messy, but I hope that at some point it will recurse to write that code also. If the process is coherent and performs in general the way I expect, I will then give it the equation that defines matter and allow it to generate the analogous sequence as a continuous stream of DNA, mRNA or proteins. It should be an easy conversion and I can then have a physicality to the computation matrix that is self generating and recursive in matter.

From there it is a matter of stretching the limits of its complexity and analyzing the results for useful methods. Since it would function from request to implementation, I should be able to define an objective and observe the solution.

Same problem different eyes

As time goes by I change and I can remember tackling many problems in my college years. I have always had an insatiable desire to learn and so I have looked into many subjects. I can remember the frustration in attempting to understand game theory, physics, chemistry and virtually everything. Chemistry was one of those things that plagued me at 18. I knew there was a way to characterize the system so that it could be considered in a rational way. I was a chemist and adding 2 gram molecular weights of on material to the same proportion of another material was certainly repeatable, but it was not a real understanding of what was taking place. It was a procedure, a devised method from experimentation and wasn't derived from an understanding of how a system operates. In fact, the system that describes chemistry is absurd in its language. There is no cause or effect outside of effect of combinations. The underlying cause is vacant. This is what troubled me most.

Now that I understand what is going on down under, that science it is coherent. It seems that the physics, and theory of matter is designed to obfuscate the underlying order. I know this isn't true, because if they understood what was really going on, they would have no gain in creating a fantasy world where they live to conceal the truth. They can only do this because they fail to grasp the entire answer.

I can relate to confusion, failure to understand, acceptable compromise, indeterminacy of process and all those other things that exist before a thing is solved.

There is a difference between how I look at problems and what others are willing to accept. It is the whole picture of the universe and many things are not possible in the small, without great consequence in the large. If the field of a particle were non-determinant at the degree that is accepted, we would see our world vacillate and effects of probability storms. For one, I know it isn't true that there is so much variability in the action of matter. I have solved the relationships and so I can say with certainty that this a nice solution that completely ignores rationality. To me the theories look like someone who throws up their hands in failure and accepts a solution that is seemingly absurd, but is workable to some extent. I experience this all the time when I code and use a new method. People explain how it is done and their understanding of the process and at times it is just wrong. So you take everything with a bit of caution and combine the opinions of several people and eventually you come to an understanding of the process.

With respect to Physics, Math, Chemistry and other mainstream sciences, they seem to take themselves a little too seriously. "Also Sprach Einstein" as if the person was infallible or even correct. I see Newton, Einstein, Maxwell,Galileo and others as great minds that contributed much to humanity in their clarity of thought and pursuit of truth, but if you want to know who I think is talented, skilled, dedicated, conscientious, consistent, and effective, it would be Brian Paul, who wrote much of the MesaGL code, AFAIK. I still can't grasp some of the concepts he manages with ease.

Teleput TelePUTT

My goal in the process of antfarmgl, code analysis, and universal understanding is to establish a self replicating framework which is cognizant and effective. The mitochondrial DNA OS is one of the necessities in the system. The ability to learn, adapt and function toward a specified goal is what is needed in the system. By teleputting at short distances I can determine if the process is consistent and repeatable and produces the desired outcome.

I watched "Destination Moon" on Google movies the other night and it was a great nostalgia and showed a time when science was changing and new ideas were being dreamed and applied. It seems that type of mind set is gone, for some reason.

I will make an attempt to describe "teleput" in simple terms that anybody should grasp. I can take a high power laser and point it at the moon and burn a smily face in the surface and thus I have "teleput" a structure. That is an absurd example and merely highlights the fact that a method can alter the structure of a remote place. I can also send a ".blend" file to a friend in China, France, Germany or Russia which allows them to recreate a 3D structure exactly as I have devised it. It can also be used as input for CNC to fabricate an object, if the material is specified. That happens at the speed of light. So I can now send a construction file at the speed of light and it can be reconstructed remotely, exactly as it is here, and conversely.

What is lacking in that scenario, which is what I am investigating, is to alter the matter at a smaller scale than a lathe, laser constructor, or mold. It uses technology that modifies the state of the atoms to make them bond in a specific way. The construction of anything depends on one single method, which is the association of two atoms through a bond of some type. The precision and specificity is the key. Once the structure and function of the universe is known in minute detail, this is quite simple. Much of the problem as it exists now with technology is the fact that a failure to understand the mechanism and process of atomic or nuclear action leads to a process which is so indeterminate that constructing systems is astoundingly complex and acts in a gross fashion with massive side effects.

Genetic systems are very conservative and specific in their action and this is their advantage. In most manufacturing systems it requires billions of time the application of energy and vastly more time to achieve a result, that a Yeast mold, such as Sacharomyces Cerevisiae, achieves many times a second, with great precision and reliability, with no manufacturing facility construction cost.

Atomic systems are said to be mostly space and though that is a reasonable analogy, they exist as a system of elements which are infinite in their size and effect. It is an overlay of infinities and it could be said that the maelstrom of interconnected space, charge, and action is calm between the eyes of the storm, but that is a relative term. The structure of matter is very specific in its action and it requires the appropriate conditions for it to change state. In the gross, fire would be the shotgun of action against the structure of matter. I guess if you apply every known and possible key to every door, a specific door will unlock .... :) , of course you unlock every other door, including the one to Pandora's playground.

It wouldn't be confusing if it wasn't new and new concepts always require some time to adapt, in the same way that I become more and more familiar with the programming tools that I use. It might seem odd or fantastic, but I heard there is a way to hit little plastic buttons and send words at the speed of light to a place where anyone in the world could read them. That may just be a science fiction story I read somewhere, it seems they called the magic process "Blah Ging", which sounds very much like a made up Klingon word from Star Trek. I suppose it could be true, but it seems too fantastic, like magic or something. It is probably just some joke.

Rasmol with a twisted sister

Today I am going to modify Rasmol to use the equation that defines the universe and see what happens. It is a good framework for this and I can use the elvi to start collecting data on PDBs to confirm my hypothesis. I have no doubts as to the conclusion of this adventure as it has already been decided by the matrix. I will then integrate it into an extension of the game I have been using as a learning template. From there, to where it always leads, somewhere else.

Good Chemistry Lectures

A play list of the lectures in Chemistry from Berkeley

I have previewed these and as far as the online courses go, this professor has a good grasp of how the molecules interact and since I just took a refresher in organic chemistry, this is very familiar. I also brings back bad memories of the fact that everybody learns IUPAC and nobody actually uses it.

This prof is far beyond my prof at a state university and that has been the main observation I take away from all the courses from Stanford, Yale, MIT, and Harvard. The quality of the courses and the clarity of their understanding of their subject makes the material come alive and many of the things that most state schools teach is far inferior in all aspects.

I had a few glitches using the new automated down loader (cclive) with (abby), but it was simply configuration issues and my hands are clean of coding dust on this one. It worked and though it is not yet a work of art, it is functional, intuitive and stable. That is where a program should stay and beauty and elegance can come with time or not for all I care. If the coders happen on this, You Rock!

The brief return of the wff

I have been studying open course ware from MIT, Harvard, Stanford, UCLA, Berkeley and others for months now. The courses range across bio-informatics, theoretical physics, networks, history, languages, chemistry, cloning, biology, genetics, matrix algebra, calculus, topology, programming, mechanical design, AI, mathematical theory, FSA, FSM, universal constructors, set theory, computer design tools, .... The constant interruptions that come from keeping up to date with what happens on the net was making it impossible to integrate what I discovered.

I discovered many things and others should take these courses.

Here are some interesting highlights and discoveries.

Something interesting about SED: the operator \2 in the substitution allows me to reference the second \(\) pair in the selection part of SED. This has nothing to do with courses, but I was fixing some stuff and learned this, which is a very useful aspect of the s function of sed.

contents of the file sedi
s/\(\s\s\)\([TRLQW][0-9]*\)\(\s\s\)/\2,/

console command
cat sed.txt| sed -f sedi



Inertia: Matter was considered to be alive and (Inert)ia means it is dead. 

Geometry: = ( Gaia metry ) or the measurement of the earth as its original meaning.

I can't even begin to relate all of the things I have learned and the consequence of that, but I will throw some interesting things out when I surface again. SAGE, scm, moinmin are things that are useful. I made an interesting discovery by relating the Egyptian "Book of the Dead" with corpus Hermiticum, Galileo, Fibonacci numbers, and some biochemistry which lead me to understand a very strange relationship about the nature of life and death itself. Imhotep the polymath.