The prototype DnaOS

It isn't new technology as nature will experiment with anything that can survive in some form or another. An example prototype is this bacteriophage at Wikipedia. The system includes all the necessary components to splice and duplicate. Another interesting link is here at Open Wet Ware.

I also found this and it is an interesting blog.

Nature does all these things, including cloning, cut and paste DNA, DNA to RNA, RNA to DNA, DNA randomizer, and even small "programs" that control the mind of the organism it infects. and many other things. It would seem that many of these things are cycling in a specific attractor and that their next leap could be to any number of associated spaces. A bacteriophage possesses all the "code" it needs to operate as an independent "operating system" and in this case it really is an operational system. It is hardware and software and data all in one physical package.

The real question is if there is an attractor which correspond to the core OS. If there is an attractor at some dimensional distance from a global minimum it can simply be pushed over the hump, so to speak, into the new operational space. What is involved is a virtually infinite dimensional problem that does have stable minimums in many dimensions. The game puzzle I created uses a series of dimensions and rotates through these dimension to depict a 3d or 4D projection of a set of dimensions. It hardly does justice to the complexity to show a 3 or even 4D representation of these logical objects. The paths through the dimensions and very interesting and I will make a tool which allows me to "turn" in any number of dimensions to view the landscape of the attractors. I will try to create a laTex document and WebGL widget that exemplifies the attractor space for biological and nuclear systems to include the interactions at the atomic level.

These attractors also exist in Nuclear and particle space. It could be said that the nucleus is the core living system. Life itself is built around the attractors which operate in that framework. Life is an extension attractor which has at its core a nuclear system. Though these systems are modeled in ISO network like layers and represented at the bond level, biological level and organism level, they are coherent from the level of the proton to the brain and existence itself in an infinite form. I am not trying to be metaphysical or mystical, I just see that all these systems interact in a quite complex way and to appreciate the operation of life, it is necessary to understand the underlying platform, which is itself very convolved, even in a single proton.

Meta-programming proteins

My interest today is meta programming as it relates to proteins. In bioinformatics of proteins the structure and thus its function is the primary concern. In a pathway that is a true universal constructor I shall calculate the structure and function of a simple life sequence loop and analyze the operation of the system in various environments. I have some tools that others lack, but they also apply in many other areas. This my interest today and I would like to devise a coherent protein meta programming that is parallel to my C language program synthesis and this way the code in generated in constructive form as well as descriptive visual form.

Mathematical system constructors like matrices are interesting, but they produce no effect in the universe ( Well, maybe the one at the link is an exception ). Constructors developed from a protein design have physical form and function to moderate the universe. I think it is a difference between starting at the counting numbers and trying to reach infinity or starting at infinity and excluding the parts that have no great significance.

The puzzle ( that is the universe ) is becoming coherent and all the pieces are falling into their places, but there still remain some issues of relationships which have no association. I guess they would be loose ends, and I need to find a place and method to connect loose ends, or at least determine a list of possible places they can connect to the matrix and then I can devise a test to see if they produce a coherent result.

I may look into making an add-on to Firefox for visualization of n-Dimensional space, just to play with it and possibly get some ideas. This is certainly the ultimate technology and an atomic level universal constructor is just what I need to teleput.(sic) It bothers me that I can't get a complete solution, but the larger problem is that when I solve something, I have to find something else to solve. I have a fairly good idea of the structure of the UC matrix and probably need to do a simple test and see what happens at different scales of action to identify things I have neglected to consider.

A new law has been passed and no individual is allowed to create copies of DNA. This means that you must inform every cell of your body of this injunction and failure to enforce the ban is considered prima facie evidence that you intend to violate the law. I personally think it is very intrusive and may violate my constitutional rights to breathe.

H1N1, Cytokine storm and liquid breathing

I had a thought when I was taking molecular genetics and cloning. I seems that perfluorocarbons could be used to stop the effects of the Cytokine storm long enough for the patient to recover. I am not a doctor and so I do not have all the information on whether this has been considered, however it seems a reasonable possibility.H1N1 and H5N1 were mentioned in the context of research years ago when I took these courses and I suggested this as a possible treatment before the current mutations made the H1N1 strain viable again. It is my opinion, however valid, that viruses will operate like a slot machine, resurfacing at intervals based on the random combination of mutations. Certainly this is purely conjecture, but it does seem a reasonable hypothesis, given the history of these naturally occurring maladies. It seems that liquid breathing was considered ( and is used ) for other purposes and never developed completely. IDK, it is so hard to know about things this complex, whether a specific thing would actually help.

Slime that thinks

This reference at Wikipedia was mentioned at arxiv and I have mentioned the fact that amoeba act with intelligence as hunters and it is no mean feat to solve what appear to be simple algorithms, "when death is on the line", or in this case eternal death for the organism that fails. That reminds me of "Princess Bride" and the Sicilian and at this link to youtube .

Intelligence in operation is poorly defined and probably that is true because what may be intelligent in one situation is stupid in another. The application must be appropriate for its environment and beyond that the utility is lost. The idea of AGI or Artificial General Intelligence is possible, but that is not universal intelligence. It would seem that a specialized intelligence would win in a specific situation and an attempt to have a device which was dominant in all scenarios would be doomed by the complexity it would require to achieve such global effectiveness.

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.

A simple answer to junk DNA

This is not a complete answer, but it is one of the elements in the solution, IMHO. As strange as it may seem, the excess of DNA could serve as a governor or throttle to the rate of growth of a cell, to enhance stability, complexity and control. A virus replicates quickly and so it sees a great deal more variety or randomness in its outcome. A slow process averages the flaws and leads to a smoother and more predictable result. The duplication of elements also allows for averaging of effect and a more consistent outcome that would be necessary for greater complexity. I suspect this is true, and I will bet 1,000 milli-cents that I am confirmed in this hypothesis within the next 40,000 years.

When pigs flu, or pigs fly

Life burns a candle exponentially by 2^t and it is the game of two exponential systems being played against each other. The flu is in an environment that is virtually homogeneous due to travel methods and number of people. I bet you could use Michaelis-Menten kinetics to model it, but it gives no answer to the problem, just a pretty graph to look at as it happens.

I am not sure and the data is not good, but it looks as if 't' in 2^t of this disease is 8 hours. That seems awfully short to me. It seems that the virus must be communicable in a matter of hours, or more likely the transfer function is not binary, which is more reasonable. So if one person can transfer the condition to 100, then 't' could be days instead of hours.

Still in multiplicity, it may replicate in a millisecond. So in reality it is a 't' of 0.01 seconds. The delay is because each of those cannot find a suitable growth medium and also are delayed in their transport. I have never done the equations or studied somebody else's and I am making it up as I go along.

I suppose I could model this, but you could also just do "Big O" of the disease and that seems to be about 10^t in days and so that would be 10 days to burn out. It is three days into this so, that means that it will be over in its first stage in 6 days. The thing that is certainly possible seems to be that once it is growing in a population of humans, it will continue to mutate in that environment. This can be bad or good as it can become less damaging or more damaging. The tendency in mutation is toward less damage for the same reason that extremely deadly diseases burn out quickly. If they kill the host, the host is not likely to further the V. So each mutation that becomes more deadly will stop itself. This is fairly consistent with history as these flus ramp up in deadliness and then back off, like a strange chaotic attractor.

These little buggers are wonderful true random number generators and they do exactly what protects somebody with open source from worst case behavior being pushed on a program, which is randomizing an algorithm so that the 'crack' and the selected algo must match, so at some point it becomes too time consuming to try and open that door.

I personally am not more or less worried, I see all things and while this is happening, California is still drifting, Yellowstone could go cataclysmic ( and certainly will some day), unnoticed asteroid hits Earth, Coronal Mass Ejection gets lucky, good match on a Γ ray burst to the Earth, magnetic reversal, solar EMP, I could go on for days naming things that are dangerous and impossible to control. The universe on any level can be a dangerous place to live.

Origins of life

This quote from scientific blogging is so true.

"No scientist has ever become a billionaire. The reason is that they have discovered a vast source of a different kind of wealth."

This is link to a series of articles on possible origin scenarios.

Language and nature

I have solved some of my problems with language by thinking this way::
When I think about or write in my personal logs about something, I use Math::curl, Sports::curl, XUL::curl, Hair::curl and so I make the terms less ambiguous by supplying some context with the word.

I have been using search patterns in models of genetic development and there is a suggestion that there may be a second form of life that is symbiotic with all cellular life. I seems that it would be the precursor of cell life. I am attempting to isolate the effect in the dependencies. I assumed it was there and I have found more supporting evidence. A Eukaryotic cell must have mitochondria to function and so it is forever linked with their evolution. I am reasonably sure that a second form of life exists as a part of all cell life, including Prokaryotes and that is flows freely between species constantly.

Some subjects are just too complex for people to understand and this is perhaps one of them. It would have emergent characteristics and like ants, the sum of simple parts can lead to a coherent organism that exists outside the physical framework.

I have also been developing some new methods to deal with chemistry and bonding. I think that present methods applied to Chemistry are very weak and outmoded. The bond definition in particular, leaves much to be desired in action and predictability. I have been making progress and some aspects of the new model are helpful.