Mitochondrial Eve and Monte Carlo Methods

The title is just something I was thinking and it occurred to me that until they have tested every single person on the planet, they will never know if they all come from the same mitochondrial tree. I also was thinking that some genes could be reversed with no effect if they were palindromes.

I had been planning to make a tree program that grows trees and various other things and this tutorial about plants is really informative. ngplant Making Trees and the second image is a snapshot of the package running and a thing I did in a few seconds of testing. The top image is one that is imported in blender from the examples. It should be very helpful in understanding the relationships. Strangely, I had assumed most of what they discovered about rotation, Fibonacci and basic model organisms. Great fun and useful too. The package assembles easily and uses "scons" and "mercurial".

Strange ways under space

Many new techniques are available for representing, managing and expressing relationships. The tikZ extension for \LaTeX is very interesting and new features of Inkscape are also useful. The combination of open source tools is advancing very rapidly. I have found them useful in expressing and understanding the complex interaction of space and energy. I have a fairly good idea of the nature of dark matter and where it originates and how it acts upon the universe. It is certainly one of those aspects for which there is no common tool or technique to measure and as such it would be virtually invisible and exists only by its disturbance of other measure. This implies the means to measure , even if only in some gross way. The coherence of information does imply some new relationships.

The understanding I now have of dark matter implies a "chemistry" which is more complex and convolved than the simple interaction of atomic bonding. Yet it does have pattern and perhaps can be placed in a type of periodic table.

Mixing math methods

Further refinement of the idea of transporting equations to action, surfaces and demonstrations in blender.

Blender allows python scripts to be transported with the blend file and can produce movies with sound and animation. It is the perfect vehicle for carrying function with data.

The simplest space

The file is a k3d surface file and the image is with conditional boundaries spaces and with surface normals. The file extension is k3ds. I have been working at resolving the sqrt(-1) as it is extended into all mathematics. There is a different perspective to all this that is less contradictory, and allows an easy progression to higher space, but it is like learning math from the ground up in a new way. It doesn't bother me as I switch from language to language all the time in programming and on the net. Sadly, this is the simplest common denominator that I can create and even this is not the whole picture. I have started doing Python in blender to allow things that are only available in other packages like numpy and even gimp or inkscape. The image is of some related surfaces that also have connectivity between them and so this is another dimension and this is just the relationship of three dimensions. I can select surfaces in the 3D space and use them in blender to analyze and comprehend the complex functional space of a signal, gravity, or system.

Name:motey
/* 
Author: motey 
*/
F():(x/y)*(x+y)+
(y/x)*(x+y)+
(x+z)*(x/z)+
(z/x)*(x+z)+
(z/y)*(z+y)+
(y/z)*(y+z)-
15*(cos(x)+
cos(y)+
cos(z))

[x]: -pi , pi
[y]: -pi , pi
[z]: -pi , pi
Cnd: (x^2 + y^2 > 3.14) &
 ( x+y+z > -3.14)
;

When the matrices are included in this it becomes even more complex and this is the foundational relationship of numerical space or measured space and sets.

It is very complex and the rule sets are complex. I see no way to resolve it to anything less simple, in fact it must be 4 infinities more complex than this just to deal with common perception.

There is quite a bit of overlap in the packages, but it seems that Python is the common denominator which can integrate them all. Perl and CPAN is another, but Perl is a little trickier and somewhat obtuse. Python seems to be structured well enough to be understandable, though it lacks speed. This is where the libraries help.

I suppose I will use the blender template with python to integrate all of the math and graphics. It has 3space and time incorporated in the design and so is closer to the manipulation of S3 in S3 and T2 in T2, but that is as close as 3 infinities, but there seems no better way to deal with it or allow visualization.

G and c fall out as it is applied to charge space and so it gives a coherent expansion of the possibilities for matter from the lowest elements to the combinations of them.

An interesting correlation is the nature of information itself and that relationship to the DNA pair AT and also GC. I could say that a specific temperature that GC is boundary and AT is open and thus the combinations of ATⁿ are the information in the same way that 0s and 1s are the foundation of binary logic.

The TED talk by Michael Shermer is very entertaining and it is an interesting equation that deals with Type 1 and Type 2 errors when Type 2 is fatal. It is worth viewing. It does get to the heart of superstition. I would add that superstition and craziness can be a survival parameter in the same way that randomness can be applied to war games to get advantage. Just because some people are illogical and insane does not mean they are absolutely destined for a Darwin award, and in fact the crazy guy and his wife who hide in a cave could be the founder of a new race if there is a global calamity that makes them selected. It seems that there is an underlying survival mechanism that is explored in the "Mote in God's Eye" and that is the "Crazy Eddie" hypothesis. And the moties is the origin of the pseudonym motey that I often use.

Trisecta

I don't know if I am missing something, but things like trisecting a line or any number division of a line with a straight edge is simple. I assume the same is true of angles or affine space. I just don't feel that it is like magic or even requires some advanced skill.

The only thing that fills me with wonder is that somebody must think it is something difficult to figure out. I surely must be missing some fact about the process.

The line is extended ( parallel ( 2 above ) ,( 1 below ) ) ( bisect lower ) and then diagonal lines are drawn. Enclosed in the circle is the original line.

I read some of the gobbledy goop of alchemists and though they can make astute observations, the problem is too complex to be characterized by a simple relationship and it just sounds like a child explaining nuclear fusion. Plato, Socrates and existentialism is also a load of dung. A person first needs to understand the universe before they can consider their relationship to it.

The image was created with Inkscape using snap to grid with Bézier curves. Elapsed time 1 minute. There are some new options to Inkscape.

I will have to investigate the math a bit to see if this holds on transformation and rotation.

I would think so at first glance, at least in Euclidian space. UNSW Linear Algebra.

Vacuum tubing of life

When looking at one type of science it is possible to apply analogous process. In vacuum tubes , a "getter" is located to remove junk atoms from a vacuum. It is my opinion that introns act as getters to save the DNA from being shredded and inactivated by a retro virus. I would assume that this originated long ago and that it also has the advantage of allowing recombining elements to create new complexity. It seems to me that in the scheme of things, if retrovirus response had not happened, complex life would not have evolved. To some extent, it is my opinion that this continuous assault on the code of life is what makes it jump from one attractor to another and causes many lethal mutants also.

The ultimate possibilities are limited by the path through the attractors, but also though the stable possibilities are limited, the complexity process can extend forever. It seems to me that this self deception that people are descended of gods and are perfect in form makes people think about immortality of individuals. I suppose this disability, ( a delusion that shreds perception of reality ) could be starting point to create the getter that changes it to something that is more consistent with reality and thus more survivable and repeatable.

The image is done with InkScape and represents the process of DNA ⇒ mRNA when introns are present. The getter acts as a target to attract a retrovirus and in this way disables its ability to integrate in a gene and thus replicate and extend its being. The funny thing is that I spoke to a retro virus the other day at the coffee shop and it claimed to be God and the chosen one in all the universe. I said that rtetroV was an idiot and it just ignored me, as I am merely some stupid bag of protein and water, and it knew it was God because it was pure and thus holy RNA.

There are many attractors in the possibility space and some seem they would be vastly more effective than a human.

CORRECTION: I have to link to this and my statement, as I was unaware of this study. and my comments here. I could be wrong, but I stand by my opinion. I will explain it this way, the first organism to have an intron would likely not have the mechanism to handle it, in that same way, variations apply as flaws first and if they are not fatal will be integrated in the process. If the action is composite in the fact that it delays replication and differentiation and serves as timing, removing 3M of 100M is 3% and would not necessarily serve as a disproof of the utility of the DNA for some other purpose. That research was 2004 and so I am the one behind on this one. I would just say I am wrong, but I am not convinced with a 3% change and I really like to see data and not conclusions. My opinion was that it produced subtle changes that affected the selection of a chaotic attractor and it is still my opinion that 3% would not necessarily be enough to cross a boundary and if mice are at 100M and human 3B, that seems to imply that perhaps it is a different situation if the amount of "junk" is 30x, in which case 3% would be only .1% change in human genome. IDK, I will research it some more.( Wikipedia claims it was 1% of mouse genome) and I think Wiki is wrong this time as the research link states 3% clearly. Other research shows that junk DNA can be lethal in other eukaryotic organisms and the mechanism of its lethality is unknown. If the DNA is non-coding in life, then what exactly is that DNA doing that can kill the organism?

I feel the test is inconclusive unless all non-coding DNA is removed. The immune system of the mouse could have changed as that is one thing that could not have been effectively measured without more knowledge of its actual operation. I will research it some more.

Another aspect of junk DNA is the fact that it can be getters which respond to specific random rotors in the viral populations. Viruses are notorious for recursing their structures and will mutate in cyclic patterns to increase their infectiousness. It would be difficult to pair up a sequence simply designed to protect against a strain which was not currently active and cycled in periods of millions of years. The junk DNA question remains unresolved for me. More research at Nature indicates that some non-coding regions are literally conserved.

Image openGL and meta UI

I have been working with scripts, ImageMagick source ( which includes the source for display ) along with the source of many other packages in an attempt to integrate all the graphical techniques as an interface through a common program structure in the complex of antfarmgl.

I also got the package:

sudo apt-get install gbrainy

Which is a Google code game that has logic puzzles. In addition I completed SuperTuxKart challenges to see what happens and if it is coherent for the complete game and discovered an interesting "Easter Egg" which I will not reference here as that would be a spoiler.

Many of the effects that can be achieved with convert can be created by loading images with display and using the menus. The clock above was sheared from the menu command.

New scripts are appearing all the time and some are very elegant. I am planning to contribute a polygon fitting algorithm that operates like this: A reverse texture lookup is used to identify areas of the image along with hole fill and a kind of image gravity. After that polygons are created in OpenGL for each element identified at a very low level. It is then rendered in 3D with lighting and then a light direction and type is fitted if possible. It proceeds through the image collecting parts in a manner similar in some aspects to a genetic polygon fitting algorithm which I saw on Robert Alsing's web log. The result uses surface geometry and lighting to further establish the coherence of the image and association of parts along with guesses of how it projects into zero space ( blackness ) or reflective blooms (100% white ) where there is no method to associate without context.

As a result, the polygons form a surface which is a 3D model and not a 2D surface such that it can technically be used as a model when it resolves. The time of completion varies widely across image types. I discovered a method to compress video files in the process and it could compress already compressed video by another 50% beyond a format like mp4 or such. I am continuing to experiment with that and may have a demo image at some time in the indeterminate infinite future.

Meta language graphic script extensions

Many scripts exist in Python , Scheme, and other languages for Gimp, Blender and other open source packages. It seems it would be possible to make a program that takes the scripts from all of the different packages and converts them to a format or language recognizable by all the programs. In this way the utilities in Gimp and Blender and Inkscape could be shared as filters. In order to test the hypothesis I am going to create a script that downloads the gimp debian package source and the inkscape source and then locates script elements , converts both directions, creates a diff and patch, then applies that to each to determine if the concept is possible.

Tree of living logic

I will make a bad pun and then explain. I think they are barking up the wrong tree. I know that the foundations of logic extends back to the Greeks and beyond that, but I wonder if they have not established a root method which can be extended to come close to the answer but never achieve the desired result as they have chosen a method which excludes an alternate concept. I cannot say that for certain at the moment and it is just a holistic sense of the issue. It is similar to attempting to mathematically characterize things which are infinite in scope. The methods must be different because the universe is inherently infinity upon infinity and no matter how long you add counting numbers you will never reach even the first infinity.

This is the problem with Physics, they determined there were two roads to take and by exclusion of the first it was obvious logic that the second is correct, the problem arises when they are well down the road and it seems very strange and it is going nowhere fast. The answer is that there must be a third or even fourth alternative that was overlooked when the decision was made and now that they are well into the wilderness, few wish to stand up and say, "I think we really f4d up.", instead they add complexity upon complexity and wander about until they happen on the main road. Just my opinion. Things can be confusing and I am not always right either. There are no absolute answers when you deal with chaos and that is what I have resigned myself to. There are some really good answers and some very useful ones, but complete certainty is just right out of the picture altogether.

I have been down this garden path many times and I always have a bad feeling about it. Some of this stuff is specious in its application and it seems a person can easily be lost in the twisty little air ducts "that all look alike" at the Hilbert Hotel. There are many people who want to be a perfect authority and that is human nature. I would certainly like to be perfect, but I have only seven toes on each foot and most people have 8 , don't they?

I am going to write a C, java and javascript implementation of this and see what I can make of the results.

I am going through this AI course at MIT [ And this one ] [ and this one ] [ and the tree around Wikipedia here ] [ and this web page ] [ and this at decision Trees .net ] [ and now I have an entire section of my local Wiki dedicated to the information and expect to export it to one of the AIs ] today and I hope to complete them before the end of the day. The goals are the same as always, to identify methods that can be contained in a chemical computing system.

Of course I have to have things ordered consistently in the directory and after scan and collect I would do this.

ls | grep "ch[0-9]_" | rename 's/ch/ch0/ '

I did discover an interesting quirk of the relationship of matter and logic which I hope will become obvious in the application of it.

It is so wonderful when all the study begins to be usable and less frustrating. I have been studying so many different things that each day seems to be filled with frustration and confusion. I decided to make a tree with `inkscape` and though this not art, it is not frustrating to work with. The familiarity with the interface and how to manage objects makes it possible to think of something and then make it real without the usual side trips into trying to figure out which thing to apply. I picked the framework of a tree at random from openclipart in perhaps the same way I might initialize a random number generator with time perhaps. So this is Image *image+=thought[i] * rand()%(treelike).

Experience builds skill

I was using InkScape again and it is funny, but I learn a couple new things each time I use anything. It becomes more pleasant and familiar as time goes by. It is not pleasant to be frustrated in trying to achieve a result. It isn't possible to fully grasp and apply a method the first time it is used. I am comfortable with InkScape, know what the icons imply, and what to expect as a result and what things to avoid. I learned that I can export in ".png" directly from the editor. I was not aware that I could do that, and I had been saving and opening the ".svg" in Gimp and then save it as ".png". This saves about 30 seconds and a dozen keystrokes and clicks for every design I make. I was able to think of the image and create it in InkScape in about 2 minutes, with very little frustration or mistake.

The image is my thinking framework for the self replicating, random expansion, AI solver. The concept of space, position, sets, orientation, selection, possibilities, handedness, size, completion, time, quality, and more. It could be days before I can make this coherent. It looks like a headache brewing and the attic cats are going to have a really heavy game of cat and mouse here. My werecats of high space will be howling too.

I have to rewrite the puzzler so it can shift the framework and complexity based on a set of complexities to match its student. I need to have puzzles of 1, 2 across in a single row, 3 across in a single row with a single solution set, and combinations that are not square or perhaps even solid geometry, or possibly in several dimensions, if my student programs get that smart.

Thinking trees

Once you define a tree method as a generic object in a 'c' program it is possible to traverse and initialize the tree in many ways to simulate some very interesting extensible solutions to common process like a calculator, regular expressions, lisp, games, AI. I was going to do a pruned decision tree of tic-tac-toe, but it got too dull and simplistic before I even finished it.

By combining linked lists, hashes, trees, and other methods I developed, it becomes a factorial expansion of capability. I think I will make a decision tree of a more complex matrix manipulation method than is currently employed that may even recurse on a matrix tree.

The image was done in Inkscape, which is SVG/XML based and in this case I did not adjust the XML before I converted it to .png with gimp.

I think I hit on something that is very critical in viewing the relationship of biological thought and simulated thought. In the case of an organism, it cannot take unlimited time to produce results and the solution, however poorly formed, must be implemented because of the "CAT AND MOUSE"( reference to stochastic matrix at wiki ) problem which deals with interacting predator prey relationships, which do not allow long choosing periods. It would be similar the fact of having to complete a render frame for a video game in 'real' time, otherwise it serves no purpose. Even if you must leave out detail, it at least achieves continuance of action.

In human perception, I believe it is inherent in the decision process that conscious event processing performs a closing operation on every open set, so that a single solution action ensues. In the case of recursion and 'If p then q' situations, it is truncated or closed and the solution is incorrect for the limited set and thus leads to confusion when it is not immediately recognized as an improper set or if it is done on purpose to conceal or obfuscate a fact in a situation that resolves in much the way the 'cat and mouse' does. Thus it is common in predator prey situations , like a lawyer manipulating a jury to influence their cognitive process in order to distort justice.

Quicksort algorithm

This is good example of how I devise algorithms without the knowledge of what is previously done. The reason I do this is to learn how to create the algorithms, and how to use them. I devised 'a type of Quicksort' with two different associated methods that speed it up. I did the algorithm in assembly language first and optimized for speed. I first used a binary partitioning on the bits from upper to lower.

The method was to create two pointers into the lists, which were beginning and end. I start with the first character of (n₀) and if it is 1 it goes 'right to the top' and if 0 it goes 'left to bottom ( actually does not move ) '. So it executes in n² as worst case. I extended the algo by merging it with some log₂(n) methods.

It sure helps to understand something, if you designed something similar. These same methods are useful in spanning trees ( like directories). I really make no difference what language or machine you use as a computer must be able to point, compare and move. Stack machines require a different algo than others, but it works out the same way.

An interesting thing I never considered is that if it is sorted, it does no swaps. This is the common case and so perhaps I did something good without knowing that I had.

It does give me a new talent to qualify code so that I can say what properties it has and make better code. Interesting thought: If I graph on the probability product of a function and analyze the applicability in frequency, it might select a different algo because it fits the most common case.

While doing this analysis I thought of something that might be a freaky new algo for sort, that is overall log₂(n). Odd, I will have to try it in my code. If it works, I will post the 'C' code.

I am adding a blackboard to my program and a method that writes characters as a path. It is just something interesting to do.

This was added to show how a high order bit binary in place sort works. It is recursive and each partition is then handled in the same way until the partitions are size 1. It finds the first !1=0 when moving a 1 and then swaps to the origin. Thus any 0 in its partition is not moved and any 1 in its partition is not moved. Mostly I am doing this to keep and enhance my XML-SVG skills and gimp. Hoping that I learn something new and faster when creating the product. It does two swaps across the entire array. I could have done an animated .gif, .avi or a .blend, but that would have been overboard, even for me, I think.

This is all great fun, but in the real world, CAM searches always take 1 cycle and the time to sort is ZERO and so it is predictable, upper=lower bound, thus Θ(n)=0 and if somebody comes up with a sort algorithm that runs in imaginary time it would win, but it is going to be tough to create a sort that runs in less than ZERO time.

I may make an CIA, FBI, DoD, or NSA show called Dumb3rs. The quality of the jokes varies by a pseudo random number and are generated with a stochastic process and picked by a Monte Carlo method using an RSA algorithm.

Blender usage

1. Collapse Arrow - Collapses modifier to show only header
2. Name Box - Stores user-definable modifier name
3. Render Display - Shows modifier effect in render
4. Interactive Display - Shows modifier effect in 3D view
5. Edit Mode Display - Shows modifier effect in edit mode
6. Cage Mode - Applies modifier to editing cage in edit mode
7. Move Up - Moves modifier up in the stack
8. Move Down - Moves modifier down in the stack
9. Delete - Removes the modifier from the stack
10. Header - Containts modifier controls
11. Apply - Makes the modifier real
12. Copy - Creates a copy of the modifier at the base of the stack
13. Sub-panel - Contains individual modifiers

Practicing my SVG, gimp and learning a little about modifiers in the process. I think 3 4 and 5 are interesting as it allows you to work faster when using models, then, really lay down some GPU cycles when you want to see the final product. The order of application is a very interesting thing that I had missed before this.(7&8)

Links to SVG and blender stuff

Just some links of stuff I have seen in the last 24.

This is a Scalable Vector Graphic animation of a clock which I think is very interesting since SVG allows you to get content(images) that you can change in every aspect, as opposed to "dot" images.

Blender for Dr Who fans, [ K9, tardid,. Daleks, ...] ( inside and out ) done in blender. This has to be somebody who does CAD work, just because of the way it is laid out.

Programming in 4 dimensions

This might seem odd if this is your first look at my blog, but taken in context it is just same old, same old. I was trying to model a program structure in Inkscape.

I found that it was not connective enough. I decided to model it in blender instead and was able to do that.

I was wondering if "GOTO" was inherently evil. I know Linus likes it, but I disagree on this one. I think "GOTO" is pure evil from the 10th dimension ( I admit the evil thing must be used, but only when faced with man eating spiders from IF hell). The drawing is what every program in the universe looks like in 4 dimensions (I use colors and numbers and texture to identify other dimensions). I have an algorithm that converts all programs into a single logical set. It has taken a long time to be able to do that. There are certain things about the nature of logic that must be satisfied in any relationship of matter. I think that good programmers have this in their minds. The problem is that it is like learning to walk. You do not have to understand gravity scientifically to walk.

The really sad thing is that I really love to program and I am teaching Alice Infinity to program. When she gets the complete hang of it, she is going to be one Godzilla effing programmer. I will only be able to use her programs or create faint imitations of her greatness for my enjoyment.

Ant Terrain

The purpose of this is to show a new technique and how easy it is to take an image ( created by SVG ( Inkscape ) and exported with gimp, in this case ) and make it into a terrain or distortion of a grid ( in blender ). This takes about 30 seconds from blender load to snapshot. This in a way is the landscape that the ( simulated ) ants perceive when searching an image. I could use a parallel image and image terrain pair that is much better for the demonstration, but it would have taken 45 seconds and I am a lazy man of few keystrokes.

These things are not additive as you might think, they are factorial combinations. If I know 1 trick it is 1 possible way of doing it. If two it can be 4 ways for two steps and 2 ways for 1 step. If number of steps is the number of options , each new technique that is mastered add factorial scale to the possibilities. I know hundreds of ways to manipulate images now and this means that the possible combinations is far beyond 10¹⁰⁰ ( a googol ). Not only do the possible combinations increase, but the effect and type of effects possible are changed. In the realm of n-Dimensional reasoning and n-Space things become very bizarre on the way to infinity.

If you are a blender head here is the link that describes in detail the simple techniques to use an image as a height map ,Okay.

Ants eat vectors

This is another aspect of the program and it is like a genetic algorithm, but more of a life algorithm. The program has ant colonies ( program threads ) that compete for food ( color vectors ), a colony has a range of action and if they find food ( their favorite color ) in the area of their nest ( center of action ) then they will include it in their hive ( associated list ) the ants compete and resolve differences between areas to determine which colony ( object list ) possesses the color vector. The same mechanisms which control ants including raiding a neighbor ant hill and taking all the food ( colors ) is determined by a set of algorithms. Colonies may slave other colonies in their area ( create linked sub object area ). Ants can be confined to the selected area from gimp or the entire image or even a specific color vector range. They can produce SVG and polygons or OpenGL textures as output or even just lists.

This is similar to a multi threaded area fill that resolves differences between areas by program weighting parameters. It also serves to be a type of program that runs against the image to extract object elements like gradients, blowout, texture, light source gradients, depth of field blurring, ...

Image decomposition

This image comes from the open clip art directory referenced on the blog page. It is remarkably simple and complex at the same time. It is a very good work of SVG art. I decided to use the techniques I have to test on this image and it is remarkable how easily it is converted from one conceptual basis to another. It is easy to see the color schemes and shadows and individual areas that are part of the whole without even using it as an SVG. It converts to polygons so easily that it is almost scary. I can have a polygon model as quick as a click.

Not only is it possible to access image conversion information, but even genotype expression variables in the character of the object space. I think that with a little work I can take an image directly from a camera and automatically identify the organism class and even correlate that information with a specific difference in the gene structure. It would be possible to essentially do a genetic sequence of the organism without even a single lab test by understanding the effect of each of the genome variables on the phenotype expression. Very odd and certainly possible.

The amount of information available is greater than the ability to effectively correlate that information into forms such as this. I think that when I have this system properly adjusted I can send it on a tour of the images on the net and it will create a relative object space that can identify patterns that are not presently known. There are many patterns that defy personal consideration due to the complexity of the data. If I can use my dimensional analysis and extend that to any number of dimensions of correlation then the patterns should just drop right out like they do with images.

This image has an axis of symmetry, 6 major polygon areas, and each of these has 2-7 sub areas that are then texture related to a limited set of textures. If you have done blender it correlates to how a person might draw this from scratch and then how a processing software can identify the parts and write a script that generates a 3D animated model of the image in a single step. It certainly makes it easier than trying to do it by hand from a complex model. What I see if I was going to do it by hand is rotate to XY axis on symmetry, split in two at symmetry line, do modeling polygons, group polygons , mirror on an axis, texture, position light, and done. I really don't need to go through the steps as I have done it enough times to be sure that I can generate this exact image as an object by "looking" at it with the computer eye.

It is very difficult to relay all the information that is contained in an image like this. For one it is the relationship of X:Y on the major axis, the angle of major lines , proportionate distortion of polygons, scale range of white dots, curvature equations of the antenna, and circular or directional vector color divergence. Each of these things becomes a dimension to measure this object image against others to determine it identity and association.

Interesting side trip into evolutionary speculation. A bug develops a useless skin flap between its leg and torso, then normally has it collapsed, but when it gets scared it spreads and scares an enemy into leaving them alone as the appear larger. As the effect changes by random mutation the surface area gets larger to present a larger image to a predator and thus more scary and more survivable. The same reflex that opens the flap could push it toward the object of fear and in this way be even more intimidating. This produces the secondary effect of moving the insect backwards and away from a strike. Now you have system of wings, a method to drive it, and with a few more random variations it becomes a flying insect. This type of surface has evolved on many different creatures and it is easy to see how it can be instantiated in any genetic line.

I see and can cause evolution of organisms in the lab. If I place an organism on a suitable growth medium and also have a less than optimum half to it, the odd, wrong transcription will eventually produce an organism that will grow in the alternate medium.

I know why a winged lion is so odd, because the set of legs that are the front of the organism must be distorted to make wings and as such, the natural progression from limb to wing is seen, but the idea that a single section of skin could go through enough change to become powered flight is virtually impossible and reflects the methods that exist in body plan expression.

Testing DNA

Testing ways to view data so I can more easily get handles and modify relationships in SVG view, 3D, and as physical objects that have computed surfaces of interaction.

This is just the SVG version and I am doing the blender version, but it takes a bit longer as I have to script some new manipulators for it.

Feel free to copy this at will, I don't go through the trouble of watermarking stuff as it is made in a few minutes and watermarking is just a waste of time.

I also need to make an automatic flow chart of the program sequences to merge here, but I think I will use this as a gate symbol for my VR interface to enter the DNA programming world.

The VR programming world is a program like an MMORPG, but in the "game" you pick and place elements and connect them to be different parts of the overall system which runs with the OpenGL VR window. It includes a Python script world also that is used to make blender objects that get automatically transferred and rendered to blender. I think I will use a Cobra with the blender icon on its head as the door to that realm. The VR tree world also controls the sequences of the Trie Thinking Tree VR and nano interface.

Worms first

The first model is worms that become ants. I have spent my time with blender and completed a survey quicker than I thought. It is oriented very much around Python associations and BPY or the linking lib that Python imports ( or equivalent action ) is the methods to interface the internals and that allows access to the information I need. I can accelerate code outside of blender and preset the things I need without fiddling with blender. I just use it as another | pipe. In terms of how biological models are created I am using the presumption that I have about how the process has advanced over time to find its current position. During embryonic development, a creature will go through the stages of diversification that lead to the organism in the first place.

The ability of a cell to recognize its peers is critical to organism coherence. The ability to recognize antithetic material is also important. My path is sphere, internal sphere has lower growth due to blocked access to nutrients, caves in, grows on the internal surface and becomes elongated torus. Contractile action is the first mechanical musculature of peristalsis. So tube worm. Then the differentiation to orientation is chemically driven by the path of contraction. Thus it is determined to have a foot that is capable of anchor and a mouth that is opposite. That is the extent of conjecture for today and then I will test it interactively in simulation and then investigate a primal form. I will block chemical pathways (in all 3 dimensions at once and in all 6 other configurations), then block ability to cohere, then add a nutrient gradient, then selectively destroy cells by nano-cauterization. I intend to search for similar research and I know that it has been done with Planaria, however I am looking for information on a more primitive worm.

The worm image is blended by curve and adjust to the shape I wanted, extrude ends, convert to vertexes, extrude flat, extrude cubic, sub-surface, scale, save. About 35 seconds of work and 15 minutes to explain it, make a captured render, save, upload to Google, insert, modify image, write this and think of a fitting mouse over. For illustrating it is vastly superior to trying to do shading in Inkscape. I can take the rendered image and convert it back to a flat for SVG, but I wonder, is it worth it unless a person does not have blender on the other end of communications.

It is not necessary to have any DNA involvement at this stage of pseudo evolution.

I also learned a few dozen new tricks for blender and will incorporate those in the Alice Infinity character. There are some great free textures that go with blender and I need to do the cloth mapping properly so I don't have to do it twice. I am taking a completely different approach to the animation as I am generating the vertexes outside blender so that I can have wrinkles and surface distortion that comes with volumetric distortion of the form. I also need to script a distance focus blurring script or find one.

I thought of a new idea just now. Forced evolution of the lower form transition by transfer and insertion of the differential DNA as a plasmid? ( electroporation and chemoporation ) I think I am correct on that, however I will see if it is necessary to test at all or whether it is obvious.

I see three major merges of large gene transfer would be likely and they would be mitochondrial, stemming, and retroviral. A good starting premise I think.