LHomme 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 thin it could be any less. !his is why practical metabiology is important. It must e"ist and we must ma e if it is to be so. #rogramming with DNA is already being done. !he molecular programming pro$ect http%&&molecular-programming.org& does it but the biophysics is un nown. DNA is thus already functioning as a programming language. Chemical reaction networ s provide a gradient on which the symbols are written. !heoretical 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 'uantum computing environment should that -- come into e"istence. (or this a clear distinction between for )eibin*ian +com-po-sa, metabiology as it currently is practically with +sampla, metabiological confidence needs sound e"ternali*ation grammetologically. --------------------------------------------------------------------------------.ut /so/ how actually is the digital universe to be comprehended biologically0 1hat are random mutations on DNA as a computer program0 Can the idea of life as software actually be e"panded beyond the notion of somatic programming 23ayr40 1hat format does this lac of structure imposed in the path of living organi*ing cause0

2!he comple" embedded control is imagined metabiologically as epigenetic modification of evolutionarily retained adaptive gene advances and sustained by fitness. !his provides the analysis of the multi-body problem involved and constrains how the syntheses can be blueboo ed. 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 e"tant. !hat however may not be what was evolutionarily detained in the organi*ation carrying forward the series to se'uence combinations.4 3ust the +bits, to be understood out of 'uantum mechanics, can they be developed as 5aufmann did modeling genetic networ s as blin ing lights, or as (eynmann thought with DNA complementation providing a basis for a difference between the two binary states, or perhaps biological digiti*ation will be understood as some actual biological reality capable of manifesting a version Chaitin6s algorithmic mutations0 In metabiology self-reproduction results from the instructions for building an organism 2von Neumann4 operated on by the same. Can the idea of assembly as a computation 21infree4 be used to inform this notion and show that active information in metabiology is reali*able even contra 7D30 1hat is the +sampla, )eibni*ian law that unites the DNA though the genetic code to the phenotype0 1hat mathematical functions synthesi*e metabiologically organi*ed instruction sets0 8ow is molecular recapitulation to be recogni*ed0 +No one really nows all the mutational mechanisms in biology, Chaitin #ractical 3etabiology % 8ow to Implement the 8alting 9racle with a computer with :rossnumbers by e"ample 2a a ;nearthing biology or how the software changes the hardware and where to find other original life4. (inding the metabiological mutational mechanism beyond simple radiation induced changes. And creating a halting oracle e'uivalent in vivo or how to associate probabilites to mutations. !he probablitiy is a function of the intrinsic rate of increase for any distribution of mutations. !his will ensure that there is seemingly a fitness increase with a non errounous and and halting change to the DNA program. !he un nowable numbers of metabiology can be thought of as grossnumerated computations from assemblies of proteins given a contingent DNA mutational history 2including epigenetics4 where forward self reproduction is the only actual infinity and the resource is simply the e"istence of life. 8ere the binary is a result of the fundamental difference between repulsion and attraction and thus there is no metaphysical reason to deny the reali*ation of theoretical metabiology practically. !he binary may be due to some other materiali*ation but on this view unlimited resource postulate is no more problematic than understanding the origin of life 2in other words how other life can self e"pand despite compressive forces4. !he cru" 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 lin as it will relate the birth of a new reproduction to the death or disintegration both with living and non-living 2virus4 things. !his has been hidden because they have e'uivalent effects on the both binaries but have different conse'uences for the ability only to NA<<91 the space that life attempts to ply

e"panding through. !his was confounded with Darwin6s +chec s, on growth and the economic analogy was not ontologically rich enough to find this understanding. !his is an inventable mathematical life form but not one that needs the same active information software fitness landscape limited by 7D3. The Basics of Theoretical Metabiology #roving theorems 2based on computability theory4 Current 3etabiology relies on the idea of artificial digitial software. If the =>st 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 2of supra-molecular substance amalgamations with coded attractions and repulsions4 and metabiology will move from theory to e"periment and then into live interfaces that can help find other life on 3ars, function in our built environment and assist in wellness during e"plorations that reach beyond 7arth. 1e will unearth the 7arth6s digital legacies as we move our population beyond its current carrying capacity. .ut first limitations of application of pure metabiology into this pra"is need to be addressed. 7D32=?>@4 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. 8ere we show how an infinity computer can resolve that argument. !he rescources need only be limited by the currently implemented grossone or two or three system manufactured. Currenly however +9ur organisms are mathematicians.,2pA=4 2not supra-molecular substance amalgamations4 +1e have a single software organism, it6s a computer program #,2pA=4 2not gene originated heritabilites subtatiated4 !his 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 selfreproductive life. 3etabiology uses however an oracle to decide if the change from one reproduction to the ne"t affects this hardware vs internal software possibility effect. .ecause the halting problem is used this functionality is contained that infinite possibility 2of not halting4 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. !his is e"actly how the notion of grossone is used and thus can be used to ma e metabiology more practical. !hus we will be

able to substitute a grossone numeral system for that lac of any algorithm that tells +us when to s ip 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 DB= process need to be D for number of base pairs in application with actual mutation0 http%&&ebi'uity.umbc.edu&blogger&=??C&>?&?A&open-problems-in-metabiology-we-are-all-randomwal s-in-program-space& +!he main idea is that the DNA underlying the morphology and behaviour of all living organisms can be considered as a form of software. !his allows for mathematical tools from computer science to be applied 2computability, algorithmic information theory, etc4 in the conte"t of random wal s within the space of all possible computer programs. !he focus here is on creating a theory that captures the cru" of biological evolution, but is well defined enough to be amenable to mathematical reasoning and proof., http%&&chofs i.tumblr.com&post&=@DAE=EE?DE&metabiology-a-mathematics-of-evolution-biology Non-mechanical non-algorthimic is 1here and when !he halting comes while the bFd and this is epistemologically such that current ecology F past evolution !here is no difference then between having a new baby life and dying the current death 2given others propagating in the legacy4. 8amming 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 'uaternions are bi2bi'uaternions4 and where&while in the digital binary biologically is e"tant. Algorithmic mutations Chaitin made the switch from thin ing of point mutations to algorithmic mutations. !his lead to the advance in thin ing of metabiology but the 'uestion remained as to what if any was the transfer of the idea to real world biology. !hey thought that this is possible via mimisis but an e"tended 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 ma ing metabiology realistic would be the introduction of rescourse limitiations., 8ere we use a rescouse grossone limited organi*ation that not only ma es metabiology more realistic but can be used to prove the e"istence of natural algorithmic mutations 2via trifold strategy of ma ing some by hand, creating hypotheses of their e"istence and searching databases for where they may be in nature4. !hus 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. (uhter the criticism of """ 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 hori*on of metabiological research. http%&&egtheory.wordpress.com&=?>=&?G&=C&proving-darwin& !his philosophical misstep can also be shown to demonstrate that social selection and cooperation!n is $ust as much as process in evolution as competition economically has been and that this can be done without group selection. Huite particularly, +#hysics simply runs the programs. If the program halts then the natural number it outputs is the program6s fitness. In other words, we have a perfectly static environment. If you were interested ecology or evolutionary game theory, then Chaitin $ust threw you out with the bath water. If you were interested in modeling, and wanted to have something computable define your fitness, then tough luc . (inally, in a fundamental biological theory, I would e"pect fitness to be something we measure when loo ing at the organisms, not a fundamental 'uantity inherent in the model. In biology, a creature simply reproduces or doesn6t, survives or doesn6tI fitness is something the observer defines when reasoning about the organisms. 1hy does Chaitin not derive fitness from more fundamental properties li e reproduction and survival0, !he notion of the rate of biotic potential as an e"ponential IJ a fundamental 'uantity inherent in models of population dynamics as a measure of fitness. !his could be replaced with compressed tetrations at an infinite limit which can provide the biological hoo to more realistic modeling onto which the mutations can be related to these changes using grossone continua of infinitesimals in the infinite species number hori*on. Jo we have an evolutionary theory that goes on forever and is not restricted to scales so large that they can not be implemented by humans studying the sub$ect. !he infinity is in the relation of the mutation to the population e"pansion 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 e"press the changes. It is from a lac of biologically motivated imagination that these critics spea .

!here are two inds of software%

Artifical Digital Joftware Computer #rograms

Natural Digital JoftwareKDNA

7wart, Dembs i and 3ar s conclude +is elegant but does not pay attention to rescourse limitation4 .ut they do not utili*e the difference between the age of artificial digital software and natural digitial software. !he 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 e"pands beyond any impact of the attractions in the conte"t of a given code that simultaneously compresses the space. !he internal attractions may function with the e"pansion to contstrain where and when e"ternal forced compressions come to bear but can not in its own tra$ectory alter the ma"imum force that might be found to be applied. !hus it is precisely the lac of resource limitation 2self-reproduction4 that enables metabiology to become practical. !his only re'uires that the grossone system be attached to an evolving system and we show this is possible with diatom evolution.

2!his shows the girdle and valve e"tensions as part of the same function4!hey are two blin ing fractals in one. !hese processes create de facto busy beaver numbers and the designed program outputs a list of these numbers that could e"ist if the diatom evolved into a different grossnumerated organon. !hus an e'uivalent to the busy beaver is possible in applied metabiology contra 7D3.

!he relation of the surface to the girdle e"tension is a catastrophe mapping of two surficial spreadabilities.

1hen a girdle mutation shows that the surface catastrophe is between two 9mega numbers then it is epigentically modified to remain while the rest are randomly methylated etc.

8ypothetical 2 Diatom 3orphological 7volution4 8ere we e"plore 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 blin ing fractal genetic regimes that produces descriptively larger and larger so enumerated valve constructions in way that might actually function biologically. !hus there is no general issue with having to have unlimited resources because the evolution that results is unlimited in terms of the morphological variation. !here 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. !he fact that actual diatom evolution may not follow the mutations hypothesi*ed to ma e the infinite fractals format does not obviate the demonstration that more realistic metabiology can not proceed without an active designer. <andom 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 organi*ations 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. !he infinity is in the ordertype or shape not the cardinality or the specific ordinal history.

1hen the valve morphologies become so small that the girdle to surface catastrophe transition can not be effected the legacy resorts to se"ual multiplication which increases the valve si*e and returns the catastrophic transition via a higher order catastrophe set. !his set is dependent on how the DNA si*e differernces change the infinitesimal surface before the girdle catastrophe seperates and is regained under 8ardy 1einberg 7'uilibrium with gamete formation and subse'uent *ygote fusation. :rossnumeral systems describes the activity of the oracle. +!o understand his first theorems in this area, you need to 2roughly4 understand the .usy .eaver problem of !ibor <ado. A good precis is here. 7ssentially, a busy beaver is a !uring machine that operates as long as possible, and then halts. !he .usy .eaver function, ..2n4, is the highest whole number produced by an n-bit busy beaver., http%&&ebi'uity.umbc.edu&blogger&=??C&>?&?A&open-problems-in-metabiology-we-are-all-randomwal s-in-program-space& 1e create a hypothetical diatom model in which the diatom creates as large a grossnumbered silicon valve and then +halts, growing and divides in half. !o created another one. 8ere the +proved, aspects of theoretical metabiology are developed e"plicitly 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 framewor different crosslineage distributions whereby some mutations growth larger enumerated structures.

up to =? All three nown forms of epigenetic inheritance are included in the model2 > loop modulation of silafins across the new smaller valve formation, structural inheritance in the form of @-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 e"change of polyamines the number and si*e of which are determined during the girdle silicon deposition and elongation.

!ransfer of metythalation pattern from silafin 2accumulated during growth and girdle vesicle e"tension4 to polyamine. #attern matching of valve vesicle by combined silafins and loose polyamines glylosocalted and sulfated vs methealated. !hus infinitesimal bit mutations in the methalyation of the silafins changes the pattern matching of valve vesicle e"pansion to the membrane. 3odel morphological relations mathematically constrained. !his series represents larger and larger grossone numerals and is the ob$ect of diatom silicon teleonomy. Jince these designs have a significant purely physioc-chemical pro"imate cause it is not ob$ectionable that a priori math orders the forms since there is lots of room for variation 2infinite4 within each format. !eleomatics is o here where teleonomy is larger yet. !hese 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. !hat is not directed but rather depends on infinitesimal mutations that are biological controllable.

3an-3ade 2DNA #rogramming4 8ere we use the same idea of grosssystem +between, generations of degradation to provide the halting oracle to DNA programming. !he infinity of cross generations is replaced into the macrothermodynamic level of organi*ation temporally.

Digital as attraction between bases. Current DNA programming does not utili*e the idea that this attraction is functional but rather tries to eliminate the +Crosstal , that past attractions succeeded. DNA is a molecular information storage system containing self-directed behaviors. !his functionality is manipulated to compute with the comple" chemical function of the system. It is an engineering discipline. It is li e using fossil plants for fuel. ;sing past forms for current energy. 1e 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. !his will be sustainable. 9ther alternatives are not. 8ere we e"plore 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. 3acrothermodyanamics determines the oracle result !his 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. !he e"tant techni'ue utili*es, 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. 8ere 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 ne"t after the logic computation and substance stability is applied. +Jpecifically, all signal strands contain a +history, domain that holds the strand in an inactive form before release from a DNA fuel comple". Jo even if we were to ma e every strand displacement step reversible, the reverse reaction of "-LM would only be able to upta e singal species that have the correct history domains for this reaction, rather than the entire population of of M which may have been generated by other reactions. 9therwise one might consider using geometry free chemical reaction networ s. 1e use instead a se'uestration of via reproduction through substance stability of those reactions with the correct +history, or generational legacy. 3etabiology in this domain is a new way to do controlled degradation of the molecular species 2eliminating the mutations that are errors or would never halt4. !he tric is to develop the geometry needed to demonstrate the metabiological concepts. 1here the halting oracle is implemented in the lower level biasing of substance stability that degrades the signal species population si*e.

8ere the infinity is infinitesimal for point by point distance but infinite with the total @ angles beyond 7arth. Natural 2 #anbiogeographic trac synthesis4 Computer Jimulated 7"perimental 3etabiology 8ere we propose the use of trac analysis and synthesis as means to search for actual alogithimic mutations by continued refinements of a time comple"ity model that matches phylogenetic patterns and biogeographic distributions. !his does a theoretical metabiology using time-comple"ity of fortran li e loops to baseline trac to phlyogenies. A certain trac -node-mass-baseline coorination can computer a certain phlogeneic tree more 'uic ly than a different coordination. 1e use this to +prove, which phylogeny evolution actually trac ed force wise. !he trac -node-mass-baseline coefficients together via the tree function enables one to define when a +mutation, 2starting with different original collection localities4 are either +clearly e'uivlalent, 2lead to the same phylo tree, or are obvious errors 2can not be used with current finite number of baselines and re'uire an infiniti*ation of the baseline number itself4. 1e use ob$ect-orinened programming as we grow this program in si*e thus simulate the idea of evo-devo subroutines on to p of subroutines. Current baseline representation represents the oracle. !hus #anbiogeographic nowledge productivity may be lin ed to the investigation of e"perimental metabiology. !his application can help to drive a cycle simultaneous development of theoretical and e"perimental metabiology.2pageC?4. Teleonomic Metabiology

3ayr rele"icologi*ied the notion of teleogy to ta e 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. 8ere 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 e"press any algorithm,2p>E4 2According to Chaitin6s revisionist history4 !his universality view derives from von Neumann6s +!he :eneral and )ogical !heory of Automata, 2p>E4 +that created the idea of fle"ible machines, universal machines, the general-purpose computer, and the distinction between software and hardware. .efore DNA was recovered biologists were considering various chemical means to thin about what divided the morphological realm into wildtypes, homo*ygotes, hetero*ygotes and mutants. !he idea is that a single lab under a communication from .renner the world of molecular biology changed into the specific idea such that +DNA contains the software for building 2and running4 the organism, an idea no common-place due to evo-devo, evolutionary developmental biology, which studies how the formation of embryos evolves. 3orphologically, metabiology forces biologists to thin that genetic differences phenotypically visible are due to differences in the software only. !hat 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. !he ey idea is self-reproduction. !his is what von Neumann thought about. (eynmann had his own version of it that was fully interpretable in biological terms. 8e discussed it as what ma es a fruit fly different than another wildtype fruit fly was simply the proteins that were e"pressed. 1hat ma es a red eyed fly baby was simply whether a certain gene as protein was e"pressed or not. A machine design that could afford such a process was a complementary system li e a hand and glove or one DNA strand and its opposite. At the time (eynmann e"pressed this view one did not now the genetic code and it was $ust thought that !8IJ idea was suffienent to generate the variety of forms developed from an embryo onward if a different letter was symboli*ed by a different place on the DNA and that this was isomorphic to the phenotypic differences via protein e"pression which was nown to ta e place through the ribsome. Jo the entire then e'uivalent of evo-devo was a translation of homo*ygotes, mutants, hetero*ygotes and wildtypes into those formats via ribosomal activity and associated biochemisty and biophysics :IN7N self-reproduction of complementary system. !his complentation is continued in metabiology in terms of a program 3 that ta es A as input and produces . as output 2program-si*e comple"ity4 relative information content. All of the biological information of (eynmann6s version is in this

Is mutation distance +9ur organisms are mathematicians, and we identify mathematical and biological creativity, page A= using :odel math 2incompleteness4 and !uring halting problem. It does not say anything about the origin of life. !his computer program calculates a number the larger the number the more fit it is. !his idea is li e 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. !his is one way to translate metabiology in to population genetics. !he dialogue on ambition of DNA programming for any teleomatics in metabiology must recogni*e that the 3olecular #rogramming pro$ect has already been involved in DNA as a universal programming language. (rom this research there are directions that DNA as various universal !uring machines can be cogni*ed. !he 8ealthy )iving 8ub at Cornell !ech could become a place where these computers are melded into tissue and printed in @D. The Future Towards a theoretical metabiology based on infinite evolutionary legacies of reca itulated rograms of coded force e! ansions com ressed by algothmic mutations" !he origin of natural digital software differences of attractions and repulsions coded through the ribsosome. 9ther 2silicon etc4 life software where to find it on 3ars0 !his origin is N9! that of 5aufmann6s blin ing lights that idea only leads to epigenetic relation 2compression to the narrowable space4 to the mutation not the origin of digitial nature of the e"pandability. .iological computation can revolve around an e"pansion of grossnumeral systems beyond one by various >-D symmetry classes connected by the D (rie*e patterns so as to ma e affordances wherein all of the OmagicO of a !uring 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 e"ist 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. !his may be desiged by lin ing the functions of the infintesimals, finites and infinites in the given computerwith differnent >-d symmetry classes by finding out the set of two-dimensional symmetry classes they reside andusing penalty coeffiencts linear*ed to a new optimum per

invention.!here is a whole new organon for instructing here but there are few with the training in thin ning in evolutio,math, and computer science capable of doing the $ob. #esign of $nfinity %om uter Software for Metabiology 7wert, 1inston, Dembs i 1illiam A., 3ar s <obert P. Active Information in 3etabiology Nolume =?>@ page >? Issue A .io-comple"ity !his might help to show that cooperation is $ust as much as process in evolution as competition economically has been and that this can be done without group selection.