View source for PlanetPhysics/Abstract Relational Biology ARB

This is a contributed topic on [[../SystemsBiology/|abstract relational biology]] and its close connections to the theory of [[../Cod/|categories]], especially the concrete and abstract categories of sets,
<math>Set</math>.

==Introduction==

''Abstract relational biology (ARB)''  is an area of mathematical or theoretical biology in which networks of linked physiological and biochemical [[../Bijective/|functions]] of living cells and multi-cellular organisms are defined over sets <math>S_i</math> and their elements <math>e_j \in S_i</math> representing for example specific metabolic products or other biomolecules; such ''organismic sets''  <math>S_i</math> are then assembled in set-related mathematical constructions-such as categories of sets- by ''making abstraction of the underlying, physical and (bio) [[../FCS3/|molecular structures]]'' that implement the cellular or physiological functions of a living organism. Thus, the early formulations of ARB by [[../NicolasRashevsky/|Nicolas Rashevsky]] were based on set theory, [[../Molecule/|molecular set theory]], and the classical logic of [[../Predicate/|predicates]] and logical propositions.
Therefore, a natural foundation for ARB would currently be the modern [[../Bijective/|relation theory]]. The relational structure of an organism is strongly emphasized over the anatomical structure and the molecular structure of cells and other components of the organism such as the chromosomes, genome, mitochondria, endoplasmic reticulum, membranes, and so on. However, the relational structure is defined in a general, mathematical sense, such as the relational structure of a category; the initial choice made by [[../RobertRosen/|Robert Rosen]] was that of the category of sets, <math>\mathbf{Set}</math> (or <math>Ens</math>). The relational structure was thus limited, both in terms of the [[../TrivialGroupoid/|objects]]' relational structure as well as in terms of the relational structures definable by [[../TrivialGroupoid/|morphisms]] that were restricted to set-theoretical mappings, or maps between sets. Subsequent developments (beginning in 1968) extended ARB to [[../TrivialGroupoid/|categories with structure]], thus not limiting ARB objects to being sets, or the morphisms to being maps between sets. Furthermore, classes were introduced instead of sets, thus not limiting the
categorical framework to [[../Cod/|small categories]].

Since 1952 there have been two major, ''set-based theories in abstract relational biology''  that are concisely outlined next.

\section{Organismic Set Theory and Abstract--Relational, \\
Metabolic--Replication, <math>(M,R)</math>--Systems}
===Brief history===
Two major proponents were Nicolas Rashevsky (up to 1973) who is one of the founders of mathematical biophysics and mathematical biology, and Robert Rosen, his former PhD student at the University of Chicago. Nicolas Rashevsky formulated the mathematical [[../TheoryOfOrganismicSets/|theory of organismic sets]] (<math>OS</math>) that are organized beginning with the genetic level, continuing to the cellular level, and then to higher levels of multi-cellular organization, activities and products; his theory was similarly formulated for societies organized at such different levels. Subsequently, it was shown that Rashevsky's organismic sets can be represented in terms of ''categories of algebraic theories''  \cite {ICB70}.

Robert Rosen introduced (metabolic--repair) models, or <math>(M,R)</math>-systems in 1957 (<ref name='RRosen1, RRosen2'/>); such [[../SimilarityAndAnalogousSystemsDynamicAdjointnessAndTopologicalEquivalence/|systems]] will be here abbreviated as <math>MR</math>-systems, (or simply <math>MR</math>'s). Rosen, then represented the <math>MR</math>'s in terms of categories of sets, deliberately selected without any structure other than the ''discrete topology of sets'' . He also considered biocomplexity to be an emergent, defining feature of organisms which is not reducible in terms of the molecular structures (or molecular components) of the organism and their physicochemical interactions.

===Basic ARB concepts===

The simplest <math>MR</math>-system represents a relational model of the primordial organism which is defined by the following ''\htmladdnormallink{categorical sequence'' {http://planetphysics.us/encyclopedia/HomologicalSequence2.html} (or [[../TrivialGroupoid/|diagram]]) of sets and set-theoretical mappings}:
<math>f: A \rightarrow B, \phi: B \rightarrow Hom_{MR}(A,B)</math>, where <math>A</math> is the set of inputs to the
<math>MR</math>-system, <math>B</math> is the set of its outputs, and <math>\phi</math> is defined as the `repair map', or <math>R</math>-component, of the <math>MR</math>-system which associates to a certain product, or output <math>b</math>, the metabolic component (such as an enzyme, E, for example)
represented by the set-theoretical mapping <math>f</math>. Then, <math>Hom_{MR}(A,B)</math> is defined as the set of all such metabolic components represented by set-theoretical) mappings <math>f</math>.
(occasionally written incorrectly as <math>\left\{f\right\}</math>)

A ''general <math>(M,R)</math>-system''  was defined by Rosen (1958a,b) as the category of the metabolic and repair components
(that were specified above in '''Definition 0.1''' ), which are networked in a complex, abstract `organism'
defined by all the abstract [[../Bijective/|relations]] and connecting maps between the sets specifying all the metabolic and repair components of such a general, abstract model of the biological organism. The morphisms of the ''<math>(M,R)</math>-system category''  are the metabolic and repair set-theoretical mappings, such as <math>f</math> and <math>\phi</math>, and its objects are the sets <math>A_i, B_i</math>, whereas <math>f \in Hom_{MR_i}(A_i,B_i)</math> and <math>\phi \in Hom_{MR_i}[B, Hom_{MR_i}(A_i,B_i)]</math>, with <math>i \in I</math>, and <math>I</math> being a finite index set, or directed set.

'''Remarks'''

With a few, additional notational changes it can be shown that the
<math>(M,R)</math>-system category is a subcategory of the [[../AAT/|category of automata]] (or [[../AAT/|sequential machines]]; <ref name='ICB73, ICBM74'/>). However, in his last published book in 1997 on ''"Essays on Life Itself"'' , Robert Rosen finally accepted the need for representing organisms in terms of ''categories with structure''  that entail biological functions, both metabolic and repair ones. Note also that, unlike Rashevsky in his theory of organismic sets, Rosen did not attempt to extend the <math>MR</math>s to modeling societies, even though with appropriate modifications, such as the introduction of Rosetta biogroupoid structures (<ref name='BBGG2k6,BBG2k7'/>) in generalized <math>(M,R)</math>-system categories with structure (<ref name='ICB70,ICB87'/>), this is feasible and yields meaningful mathematical and sociological results.

==All Sources==
<ref name='Rashevsky1-yr1965'/>
<ref name='Rashevsky2-1969'/>
<ref name='ICB70'/>
<ref name='ICB73'/>
<ref name='ICBM74'/>
<ref name='ICB6'/>
<ref name='ICB2'/>
<ref name='ICB87'/>
<ref name='BBGG2k6'/>
<ref name='Rosenbook'/>
<ref name='RRosen1'/>
<ref name='RRosen2'/>
<ref name='RRosen3'/>

==References==
<references>

</ref><ref name='Rashevsky1-yr1965'>
Rashevsky, N.: 1965, The Representation of Organisms in Terms of
Predicates, ''Bulletin of Mathematical Biophysics''  '''27''' : 477-491.

</ref><ref name='Rashevsky2-1969'>
Rashevsky, N.: 1969, Outline of a Unified Approach to Physics, Biology and Sociology., ''Bulletin of Mathematical Biophysics''  '''31''' : 159--198.

</ref><ref name='ICB70'>
Baianu, I.C.: 1970, Organismic Supercategories: II. On Multistable Systems.,''Bulletin of Mathematical Biophysics'' , '''32''' : 539-561.

</ref><ref name='ICB73'>
Baianu, I.C., Some Algebraic Properties of <math>(M,R)</math>--systems.,
''Bulletin of Mathematical Biophysics'' , '''35''' : 318-323.

</ref><ref name='ICBM74'>
Baianu, I.C. and M.M. Marinescu. 1974. On a Functorial Construction of <math>(M,R)</math>--systems. ''Rev. Roumaine Math.'' , 215-224.

</ref><ref name='ICB6'>
Baianu, I.C.: 1977, A Logical Model of Genetic Activities in \L ukasiewicz Algebras: The Non-linear Theory.,
''Bulletin of Mathematical Biology'' , '''39''' : 249-258.

</ref><ref name='ICB2'>
Baianu, I.C.: 1980, Natural Transformations of Organismic Structures., ''Bulletin of Mathematical Biology'' ,'''42''' : 431-446.

</ref><ref name='ICB87'>
Baianu, I.C.: 1987. ''Mathematical Models in Medicine'' , vol. 7., Ch.11 Pergamon Press, New York, 1513 -1577;
URLs: ''CERN Preprint No. EXT-2004-072:'' ,
[http://doc.cern.ch//archive/electronic/other/ext/ext-2004-072.pdf available here as PDF], or
[http://en.scientificcommons.org/1857371 as as an archived html document].

</ref><ref name='BBGG2k6'>
Baianu I. C., Brown R., Georgescu G. and J. F. Glazebrook: 2006b, Complex Nonlinear Biodynamics in Categories, Higher Dimensional Algebra and \L ukasiewicz--Moisil Topos: Transformations of Neuronal, Genetic and Neoplastic Networks., ''Axiomathes'' , '''16'''  Nos. 1--2: 65--122.

</ref><ref name='Rosenbook'>
Rosen, R.: 1985, ''Anticipatory Systems'' , Pergamon Press: New York.

</ref><ref name='RRosen1'>
Rosen, R.: 1958a, A Relational Theory of Biological Systems., ''Bulletin of Mathematical Biophysics''
'''20''' : 245-260.

</ref><ref name='RRosen2'>
Rosen, R.: 1958b, The Representation of Biological Systems from the Standpoint of the
Theory of Categories., ''Bulletin of Mathematical Biophysics''  '''20''' : 317-341.

</ref><ref name='RRosen3'>
Rosen, R.: 1987, On Complex Systems, ''European Journal of Operational Research''  '''30''' :129--134.

</ref></references>

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