L’Homme Software_____

If man is indeed software then it must be true that, the principle idea of metabiology – that DNA is a universal programming language - - it must be true. Chaitin does not think it could be any less. This is why practical metabiology is important. It must exist and we must make if it is to be so.

Programming with DNA is already being done. The molecular programming project

http://molecular-programming.org/ does it but the biophysics is unknown.

DNA is thus already functioning as a programming language. Chemical reaction networks provide a gradient on which the symbols are written.

Theoretical universality is however a very far cry from actual global applicability as there is nothing to suggest that biological software will compete with electronic software, nor even with a future quantum computing environment should that -- come into existence.

For this a clear distinction between for Leibinzian “com-po-sa” metabiology as it currently is practically with “sampla” metabiological confidence needs sound externalization grammetologically.

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But …so… how actually is the digital universe to be comprehended biologically?

What are random mutations on DNA as a computer program?

Can the idea of life as software actually be expanded beyond the notion of somatic programming (Mayr)?

What format does this lack of structure imposed in the path of living organizing cause?

(The complex embedded control is imagined metabiologically as epigenetic modification of evolutionarily retained adaptive gene advances and sustained by fitness. This provides the analysis of the multi-body problem involved and constrains how the syntheses can be blue-booked. I hope this is enough of a developmental constraint that not only does the phylogeny recapitulates that ontogeny but the teleonomy must subordinate any possible teleomatic naturally extant. That however may not be what was evolutionarily detained in the organization carrying forward the series to sequence combinations.)

Must the “bits” to be understood out of quantum mechanics, can they be developed as Kaufmann did modeling genetic networks as blinking lights, or as Feynmann thought with DNA complementation providing a basis for a difference between the two binary states, or perhaps biological digitization will be understood as some actual biological reality capable of manifesting a version Chaitin’s algorithmic mutations?

In metabiology self-reproduction results from the instructions for building an organism (von Neumann) operated on by the same. Can the idea of assembly as a computation (Winfree) be used to inform this notion and show that active information in metabiology is realizable even contra EDM? What is the “sampla” Leibnizian law that unites the DNA though the genetic code to the phenotype? What mathematical functions synthesize metabiologically organized instruction sets? How is molecular recapitulation to be recognized?

“No one really knows all the mutational mechanisms in biology” Chaitin

Practical Metabiology : How to Implement the Halting Oracle with a computer with Grossnumbers by example (aka Unearthing biology or how the software changes the hardware and where to find other original life). Finding the metabiological mutational mechanism beyond simple radiation induced changes. And creating a halting oracle equivalent in vivo or how to associate probabilites to mutations. The probablitiy is a function of the intrinsic rate of increase for any distribution of mutations. This will ensure that there is seemingly a fitness increase with a non errounous and and halting change to the DNA program.

The unknowable numbers of metabiology can be thought of as grossnumerated computations from assemblies of proteins given a contingent DNA mutational history (including epigenetics) where forward self reproduction is the only actual infinity and the resource is simply the existence of life. Here the binary is a result of the fundamental difference between repulsion and attraction and thus there is no metaphysical reason to deny the realization of theoretical metabiology practically. The binary may be due to some other materialization but on this view unlimited resource postulate is no more problematic than understanding the origin of life (in other words how other life can self expand despite compressive forces). The crux is in how mutations affect or effect the copying of the instructions in some way from abiotic to biotic aggregations. Interestingly the cell will turn out to be this biological link as it will relate the birth of a new reproduction to the death or disintegration both with living and non-living (virus) things. This has been hidden because they have equivalent effects on the both binaries but have different consequences for the ability only to NARROW the space that life attempts to ply expanding

through. This was confounded with Darwin’s “checks” on growth and the economic analogy was not ontologically rich enough to find this understanding. This is an inventable mathematical life form but not one that needs the same active information software fitness landscape limited by EDM.

The Basics of Theoretical Metabiology – Proving theorems (based on computability theory)

Current Metabiology relies on the idea of artificial digitial software. If the 21st century is going to be the time of techno-bio hub creation then this artificial digital software world will be replaced by a natural digital software world (of supra-molecular substance amalgamations with coded attractions and repulsions) and metabiology will move from theory to experiment and then into live interfaces that can help find other life on Mars, function in our built environment and assist in wellness during explorations that reach beyond Earth. We will unearth the Earth’s digital legacies as we move our population beyond its current carrying capacity. But first limitations of application of pure metabiology into this praxis need to be addressed. EDM(2013) suggest that any applied metabiology will not be able to use the proven basis wherein the very rescourse limitation scenario that wsa used to garner the proof is used to implement the practice. Here we show how an infinity computer can resolve that argument. The rescources need only be limited by the currently implemented grossone or two or three system manufactured.

Currenly however

“Our organisms are mathematicians.”(p42) (not supra-molecular substance amalgamations)

“We have a single software organism, it’s a computer program P”(p42) (not gene originated heritabilites subtatiated)

This computer program calculates a number – the larger the number the more fit it is.

The self-reproduction is simply the output (number) which is used to create a larger number of the next organism. Thus a number via the program. One makes random changes to the program and than recalculates the number. So this is an organism that has a hardware change caused software alteration or simply an external (not internal program) software alteration that results during growth and development into a different allometric form of the phenotype as a number difference.

(thus it cannot be a change in the ribosome (internal forced change)(we will see cases where an internal change can be the mutation provided it does not affect the relation of the oracle to the fitness).That will bear on the force relations that have to do with the origin of self-reproductive life.

Metabiology uses however an oracle to decide if the change from one reproduction to the next affects this hardware vs internal software possibility effect. Because the halting problem is used this functionality is contained that infinite possibility (of not halting) and one must use the oracle when determining whether a mutation simply produces a number or does something other which disables the program relative to the fitness measure. This is exactly how the notion of grossone is used and thus can be used to make metabiology more practical. Thus we will be able to substitute a grossone numeral system for that lack of any algorithm that tells “us when to skip a mutation or an organism that never

halts.” If the new organism can not be gross numbered in the currently pedigreed system the evolutionary legacy ends even though with a different hardware or internal change it may be possible.

Does D^2 process need to be D for number of base pairs in application with actual mutation?

http://ebiquity.umbc.edu/blogger/2009/10/04/open-problems-in-metabiology-we-are-all-random-walks-in-program-space/

“The main idea is that the DNA underlying the morphology and behaviour of all living organisms can be considered as a form of software. This allows for mathematical tools from computer science to be applied (computability, algorithmic information theory, etc) in the context of random walks within the space of all possible computer programs. The focus here is on creating a theory that captures the crux of biological evolution, but is well defined enough to be amenable to mathematical reasoning and proof.”

http://chofski.tumblr.com/post/23748288078/metabiology-a-mathematics-of-evolution-biology

Non-mechanical – non-algorthimic is

Where and when The halting comes while the b=d and this is epistemologically such that current ecology = past evolution

There is no difference then between having a new baby life and dying the current death (given others propagating in the legacy).

Hamming distances can not find these points as they are not ones that can be described

with vector analysis but instead are found algebraically where diverging quaternions are bi(biquaternions) and where/while in the digital binary biologically is extant.

Algorithmic mutations

Chaitin made the switch from thinking of point mutations to algorithmic mutations. This lead to the advance in thinking of metabiology but the question remained as to what if any was the transfer of the idea to real world biology. They thought that this is possible via mimisis but an extended view of the relation of biology to physics, math and philosophy via force should allow one to see this connection.

“Chaitin notes that as his metabiology is made more biologically realistic he will probably be unable to prove results and instead have to be content with simulation. It seems that the first step toward making metabiology realistic would be the introduction of rescourse limitiations.”

Here we use a rescouse grossone limited organization that not only makes metabiology more realistic but can be used to prove the existence of natural algorithmic mutations (via trifold strategy of making some by hand, creating hypotheses of their existence and searching databases for where they may be in nature). Thus despite the nature of the oracle the mere postulation of a new empricial entity that relates mutation to evolutionary heritages is enough to guarantee a successful implementiaion of a more biologically realistic metabiology. Fuhter the criticism of xxx is also thus demonstrated to be

undfounded and simply results from a confusion on the relation of philosophy, to physics to the forces that unfold biological organons which instruct the future horizon of metabiological research.

http://egtheory.wordpress.com/2012/06/29/proving-darwin/

This philosophical misstep can also be shown to demonstrate that social selection and cooperationTn is just as much as process in evolution as competition economically has been and that this can be done without group selection.

Quite particularly,

“Physics simply runs the programs. If the program halts then the natural number it outputs is the program’s fitness. In other words, we have a perfectly static environment. If you were interested ecology or evolutionary game theory, then Chaitin just threw you out with the bath water. If you were interested in modeling, and wanted to have something computable define your fitness, then tough luck. Finally, in a fundamental biological theory, I would expect fitness to be something we measure when looking at the organisms, not a fundamental quantity inherent in the model. In biology, a creature simply reproduces or doesn’t, survives or doesn’t; fitness is something the observer defines when reasoning about the organisms. Why does Chaitin not derive fitness from more fundamental properties like reproduction and survival?”

The notion of the rate of biotic potential as an exponential IS a fundamental quantity inherent in models of population dynamics as a measure of fitness. This could be replaced with compressed tetrations at an infinite limit which can provide the biological hook to more realistic modeling onto which the mutations can be related to these changes using grossone continua of infinitesimals in the infinite species number horizon.

So we have an evolutionary theory that goes on forever and is not restricted to scales so large that they can not be implemented by humans studying the subject. The infinity is in the relation of the mutation to the population expansion which is also an infinity of heritages goeing forward as well as an infinity with respect to the origin o f the coded life that express the changes. It is from a lack of biologically motivated imagination that these critics speak.

There are two kinds of software:

Artifical Digital Software – Computer Programs Natural Digital Software—DNA

Ewart, Dembski and Marks conclude “is elegant but does not pay attention to rescourse limitation)

But they do not utilize the difference between the age of artificial digital software and natural digitial software. The grossone numeral system which contains both infinity and infintesimals however is able to acess this difference and provide a means once programmed to implement practical metabiology on current computers. Changing an increaseing number of bits is dependent on the how much repulsive space expands beyond any impact of the attractions in the context of a given code that simultaneously compresses the space. The internal attractions may function with the expansion to contstrain where and when external forced compressions come to bear but can not in its own trajectory alter the maximum force that might be found to be applied.

Thus it is precisely the lack of resource limitation (self-reproduction) that enables metabiology to become practical. This only requires that the grossone system be attached to an evolving system – and we show this is possible with diatom evolution.

(This shows the girdle and valve extensions as part of the same function)They are two blinking fractals in one. These processes create de facto busy beaver numbers and the designed program outputs a list of these numbers that could exist if the diatom evolved into a different grossnumerated organon. Thus an equivalent to the busy beaver is possible in applied metabiology contra EDM.

The relation of the surface to the girdle extension is a catastrophe mapping of two surficial spreadabilities.

When a girdle mutation shows that the surface catastrophe is between two Omega numbers then it is epigentically modified to remain while the rest are randomly methylated etc.

Hypothetical ( Diatom Morphological Evolution) Here we explore the use of grossone to model the morphological variability in diatom shell shapes and describe a hypothetical epigenetic process that facilitates the combination of two blinking fractal genetic regimes that produces descriptively larger and larger so enumerated valve constructions in way that might actually function biologically. Thus there is no general issue with having to have unlimited resources because the evolution that results is unlimited in terms of the morphological variation. There is a limit when the evolution never halts or has obvious errors but these can be overcome with increase in the infinity that binds the infinitesimal girdle difference to the infinite surface difference. The fact that actual diatom evolution may not follow the mutations hypothesized to make the infinite fractals format does not obviate the demonstration that more realistic metabiology can not proceed without an active designer. Random epigenetic changes are all that are needed for this metabiological application to proceed and succeed. All infinite divisions do not need to be tried because only those grossone organizations that are compatible the historical gross system numeration legacy go forward with the resources however they are. A certain level of silicon etc is needed but an infinite amount is not. The infinity is in the ordertype or shape not the cardinality or the specific ordinal history.

When the valve morphologies become so small that the girdle to surface catastrophe transition can not be effected the legacy resorts to sexual multiplication which increases the valve size and returns the catastrophic transition via a higher order catastrophe set. This set is dependent on how the DNA size differernces change the infinitesimal surface before the girdle catastrophe seperates and is regained under Hardy Weinberg Equilibrium with gamete formation and subsequent zygote fusation.

Grossnumeral systems describes the activity of the oracle.

“To understand his first theorems in this area, you need to (roughly) understand the Busy Beaver problem of Tibor Rado. A good precis is here. Essentially, a busy beaver is a Turing machine that operates as long as possible, and then halts. The Busy Beaver function, BB(n), is the highest whole number produced by an n-bit busy beaver.”

http://ebiquity.umbc.edu/blogger/2009/10/04/open-problems-in-metabiology-we-are-all-random-walks-in-program-space/

We create a hypothetical diatom model in which the diatom creates as large a grossnumbered silicon valve and then “halts” growing and divides in half. To created another one.

Here the “proved” aspects of theoretical metabiology are developed explicitly in a model of diatom morphological evolution where larger and larger numbers describe different silicon structures which obtain in different lineages as infinitesimal mutations to the building process provide within an infinite framework different crosslineage distributions whereby some mutations growth larger enumerated structures.

up to 20

All three known forms of epigenetic inheritance are included in the model( 1 loop modulation of silafins across the new smaller valve formation, structural inheritance in the form of 3-D pattern matching between separating daughter cells, and chromatin associated meyhtalation that is converted between silafins and other proteins later attached to the scaffold via exchange of polyamines the number and size of which are determined during the girdle silicon deposition and elongation.

Transfer of metythalation pattern from silafin (accumulated during growth and girdle vesicle extension) to polyamine. Pattern matching of valve vesicle by combined silafins and loose polyamines glylosocalted and sulfated vs methealated. Thus infinitesimal bit mutations in the methalyation of the silafins changes the pattern matching of valve vesicle expansion to the membrane.

Model morphological relations mathematically constrained. This series represents larger and larger grossone numerals and is the object of diatom silicon teleonomy. Since these designs have a significant purely physioc-chemical proximate cause it is not objectionable that a priori math orders the forms since there is lots of room for variation (infinite) within each format. Teleomatics is ok here where teleonomy is larger yet. These ordinal formats grossone manifested vary in the forces needed to envelope them and thus do not represent the evolutionary forces that give rise to them. That is not directed but rather depends on infinitesimal mutations that are biological controllable.

Man-Made (DNA Programming) Here we use the same idea of grosssystem “between” generations of degradation to provide the halting oracle to DNA programming. The infinity of cross generations is replaced into the macrothermodynamic level of organization temporally.

Digital as attraction between bases.

Current DNA programming does not utilize the idea that this attraction is functional but rather tries to eliminate the “Crosstalk” that past attractions succeeded.

DNA is a molecular information storage system containing self-directed behaviors. This functionality is manipulated to compute with the complex chemical function of the system. It is an engineering discipline.

It is like using fossil plants for fuel. Using past forms for current energy. We ne a design within this past legacy that derives its energy or computation from within the format historically changing and thus to have a human future in sync with a living past. This will be sustainable. Other alternatives are not.

Here we explore the view of DNA as software, the notion of DNA as a programming language where toe hold mediated branch migrations permit the design of and construction of computations with DNA and apply the idea of substance stability to find larger and larger supramolecular computed structures that substitute for the notion of Algorithmic mutations. Macrothermodyanamics determines the oracle result

This can help to drive metabiology into the realm of a new technology of DNA programmable technology and assist in changing the relation of communication, built environment and living well hubs.

The extant technique utilizes” logically reversible computation” provided by adding and removing monomers from DNA polymer ends through toe-hold mediated branch migration. It is a method of embedding logic control into biological and chemical systems.

Here we combine this process with an interface that interacts with self-reproducing biological systems under macrothermodyamically enginerred constraints so as to afford man-made algorithmic mutations where the “organim” is the supramolecular structure replicated from one “generation” to the next after the logic computation and substance stability is applied.

“Specifically, all signal strands contain a “history” domain that holds the strand in an inactive form before release from a DNA fuel complex. So even if we were to make every strand displacement step reversible, the reverse reaction of x->Y would only be able to uptake singal species that have the correct history domains for this reaction, rather than the entire population of of Y which may have been generated by other reactions.

Otherwise one might consider using geometry free chemical reaction networks. We use instead a sequestration of via reproduction through substance stability of those reactions with the correct “history” or generational legacy. Metabiology in this domain is a new way to do controlled degradation of the molecular species (eliminating the mutations that are errors or would never halt).

The trick is to develop the geometry needed to demonstrate the metabiological concepts. Where the halting oracle is implemented in the lower level biasing of substance stability that degrades the signal species population size.

Here the infinity is infinitesimal for point by point distance but infinite with the total 3 angles beyond Earth.

Natural ( Panbiogeographic track synthesis) Computer Simulated Experimental Metabiology - Here we propose the use of track analysis and synthesis as means to search for actual alogithimic mutations by continued refinements of a time complexity model that matches phylogenetic patterns and biogeographic distributions.

This does a theoretical metabiology using time-complexity of fortran like loops to baseline track to phlyogenies. A certain track-node-mass-baseline coorination can computer a certain phlogeneic tree more quickly than a different coordination. We use this to “prove” which phylogeny evolution actually tracked force wise. The track-node-mass-baseline coefficients together via the tree function enables one to define when a “mutation” (starting with different original collection localities) are either “clearly equivlalent” (lead to the same phylo tree” or are obvious errors (can not be used with current finite number of baselines and require an infinitization of the baseline number itself). We use object-orinened programming as we grow this program in size thus simulate the idea of evo-devo subroutines on to p of subroutines.

Current baseline representation represents the oracle.

Thus Panbiogeographic knowledge productivity may be linked to the investigation of experimental metabiology. This application can help to drive a cycle simultaneous development of theoretical and experimental metabiology.(page90).

Teleonomic Metabiology

Mayr relexicologizied the notion of teleogy to take account of in part of recent advances in computation brought on by computers dividing it into a human etc. purposive activity, a teleomatics and a teleonomy. Here we show how metabiology creates different telonomies via human designed products given different relations catalytically to underlying teleomatics or not.

“DNA is presumably a universal programming language, one that is sufficiently powerful to express any algorithm”(p18)

(According to Chaitin’s revisionist history) This universality view derives from von Neumann’s “The General and Logical Theory of Automata” (p18) “that created the idea of flexible machines, universal machines, the general-purpose computer, and the distinction between software and hardware.

Before DNA was recovered biologists were considering various chemical means to think about what divided the morphological realm into wildtypes, homozygotes, heterozygotes and mutants.

The idea is that a single lab under a communication from Brenner the world of molecular biology changed into the specific idea such that “DNA contains the software for building (and running) the organism, an idea no common-place due to evo-devo, evolutionary developmental biology, which studies how the formation of embryos evolves.

Morphologically, metabiology forces biologists to think that genetic differences phenotypically visible are due to differences in the software only. That the hardware the program runs on is not part and parcel of the form developing as the algothrimioc mutations are selected and the mathematical organism becomes more fit.

The key idea is self-reproduction. This is what von Neumann thought about. Feynmann had his own version of it that was fully interpretable in biological terms. He discussed it as what makes a fruit fly different than another wildtype fruit fly was simply the proteins that were expressed. What makes a red eyed fly baby was simply whether a certain gene as protein was expressed or not. A machine design that could afford such a process was a complementary system – like a hand and glove or one DNA strand and its opposite. At the time Feynmann expressed this view one did not know the genetic code and it was just thought that THIS idea was suffienent to generate the variety of forms developed from an embryo onward if a different letter was symbolized by a different place on the DNA and that this was isomorphic to the phenotypic differences via protein expression which was known to take place through the ribsome. So the entire then equivalent of evo-devo was a translation of homozygotes, mutants, heterozygotes and wildtypes into those formats via ribosomal activity and associated biochemisty and biophysics GIVEN self-reproduction of complementary system.

This complentation is continued in metabiology

in terms of a program M that takes A as input and produces B as output (program-size complexity) – relative information content.

All of the biological information of Feynmann’s version is in this

Is mutation distance

“Our organisms are mathematicians, and we identify mathematical and biological creativity” page 42 using Godel math (incompleteness) and Turing halting problem.

It does not say anything about the origin of life.

This computer program calculates a number – the larger the number the more fit it is.

This idea is like that where the “intrinsic biotic population growth rate potential” was modled as a measure of fitness such that a larger r meant a more fit population. This is one way to translate metabiology in to population genetics.

The dialogue on ambition of DNA programming for any teleomatics in metabiology must recognize that the Molecular Programming project has already been involved in DNA as a universal programming language.

From this research there are directions that DNA as various universal Turing machines can be cognized.

The Healthy Living Hub at Cornell Tech could become a place where these computers are melded into tissue and printed in 3D.

The Future – Towards a theoretical metabiology based on infinite evolutionary legacies of recapitulated programs of coded force expansions compressed by algothmic mutations.

The origin of natural digital software – differences of attractions and repulsions coded through the ribsosome. Other (silicon etc) life software – where to find it on Mars? This origin is NOT that of Kaufmann’s blinking lights – that idea only leads to epigenetic relation (compression to the narrowable space) to the mutation not the origin of digitial nature of the expandability.

Biological computation can revolve around an expansion of grossnumeral systems beyond

one by various 1-D symmetry classes connected by the 7 Frieze patterns so as to make

affordances wherein all of the "magic" of a Turing machine is fleshed into new functionalities

of concurrency, interaction, continuous data as the mental-recursions of metabiology meet practical DNA programming. A given infinity computer must be able to interact biologically with the model it simulates. It needs to be able be the place the instruction is both connatively inserted and denotated biophysically topologically. Concurrencies may exist differently for infinite process of different length and continuous data must find a way to enter the the numbers that repeat in any given recursion.

This may be desiged by linking the functions of the infintesimals, finites and infinites in the given computerwith differnent 1-d symmetry classes by finding out the set of two-dimensional symmetry classes they reside andusing penalty coeffiencts linearzed to a new optimum per invention.There is a whole new organon for instructing here but there are few with the training in thinkning in evolutio,math, and computer science capable of doing the job.

Design of Infinity Computer Software for Metabiology

Ewert, Winston, Dembski William A., Marks Robert J. Active Information in Metabiology Volume 2013 page 10 Issue 4 Bio-complexity

This might help to show that cooperation is just as much as process in evolution as competition economically has been and that this can be done without group selection.