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===Categorical dynamics and mathematical representations in functional biology===
''Functional biology''  is mathematically represented through models of integrated biological [[../Bijective/|functions]] and activities that are expressed in terms of mathematical [[../Bijective/|relations]] between the metabolic and repair components (Rashevsky, 1962 <ref name='NR62'/>). Such [[../CategoricalGroupRepresentation/|representations]] of complex biosystems, mappings/functions, as well as their super-complex [[../MathematicalFoundationsOfQuantumTheories/|dynamics]] are important for understanding physiological dynamics and functional biology in terms of [[../ModuleAlgebraic/|algebraic topology]] [[../PreciseIdea/|concepts]], concrete [[../Cod/|categories]], and/or [[../Cod/|graphs]]; thus, they are describing or modeling theost important
inter-relations of biological functions in living organisms. This approach to biodynamics in terms of
[[../TrivialGroupoid/|category theory]] representations of biological functions is part of the broader [[../CosmologicalConstant/|field]] of ''categorical dynamics'' .

In order to establish mathematical relations, or laws, in biology one needs to define the key concept of
''mathematical representations'' . A general definition of such representations as utilized by mathematical or theoretical biologists, as well as mathematical physicists, is specified next together with well-established mathematical examples.

''Mathematical representations''  are defined as \emph{associations <math>\Re : S^* \to C </math>
between abstract structures <math>S^*</math> and classes <math>C</math>, or sets (<math>S</math>) of concrete structures <math>S_c</math>}, often satisfying
several additional conditions, or axioms imposed by the mathematical context (or category) to whom
the abstract structures <math>S^*</math> belong. Thus, in ''representation theory''  one is concerned with various collections
of quantities which are similar to the abstract structure in regard to one or several mathematical [[../Cod/|operations]].

'''Notes.'''  ''Abstract structures''  are employed above in the sense defined by Bourbaki (1964) <ref name='NB64'/>.
Unlike ''abstract categories''  that may have only [[../TrivialGroupoid/|morphisms]] (or arrows) and `no [[../TrivialGroupoid/|objects]]' (or vertices), other ''abstract structures''  are simply defined as `pure' [[../CoIntersections/|algebraic]] objects with
no numerical content or direct physical interpretation, whereas the ''concrete structures''  do have
either a numerical content or a direct physical interpretation.

'''Examples'''

#An abstract [[../TopologicalOrder2/|symmetry group]], <math>G</math> with multiplication "<math>\cdot</math>" has mathematical representations by [[../Matrix/|matrices]], or numbers, that have the "same multiplication table"  as the [[../TrivialGroupoid/|group]] (McWeeny, 2002 <ref name='RMcW2k2'/>). In this example, such ''similarity in structure''  is called a ''[[../TrivialGroupoid/|homomorphism]]''. As a specific illustration consider the symmetry group <math>C_{3v}</math> that admits a numerical representation by the sextet of numbers <math>(1,1,1,-1,-1,-1)</math> (or line matrix)
for the group symmetry elements <math>(E, C_3, \bar{C}_3, \sigma_1, \sigma_2, \sigma_3)</math>, where the latter
five are rotations (or the ''[[../Generator/|generators]]'' of this symmetry group) and <math>E</math> is the ''unit element''  of the
group. Note that the symmetry group <math>C_{3v}</math> has the obvious ''geometric''  interpretation as the
collection of ''symmetry operations''  of an equilateral triangle. Such symmetry operations are defined by
the abstract group elements, with the group unit element playing the role of the `[[../Cod/|identity]] symmetry operation'
that leaves any physical object (or space on which it acts) unchanged, such as a <math>360</math> degree rotation in three-dimensional (real) space. Note that each such symmetry operation of the symmetry group has an ''inverse''  which `cancels out' exactly the action of its opposite symmetry operation (e.g., <math>C_3</math> and <math>\bar{C}_3</math>),
and of course, multiplication by <math>E</math> leaves all symmetry operations unchanged. (This is also true for ''\htmladdnormallink{non-Abelian'' {http://planetphysics.us/encyclopedia/AbelianCategory3.html}, or [[../AbelianCategory3/|noncommutative]]} groups with <math>E</math> acting either on the ''left''  or on the ''right''  of all the other group operations).

#The previous example extends to abstract [[../QuantumOperatorAlgebra5/|groupoids]] <math>\grp</math> whose representations are, however, defined as
''morphisms (or \htmladdnormallink{functors'' {http://planetphysics.us/encyclopedia/TrivialGroupoid.html})}, to either ''families''  or ''fiber bundles''  of spaces- such as [[../NormInducedByInnerProduct/|Hilbert spaces]] <math>\H</math>. Moreover, one notes that groupoids exhibit both ''internal''  and ''external''  symmetries
(''viz.''  Weinstein, 1998). Whereas a group can be considered as a ''one object''  category with all invertible
morphisms, a groupoid can be defined as a category with all invertible morphisms but with ''many objects''  instead of just one. Therefore, the groupoid structure has a substantial advantage over the group structure
as it allows for the simultaneous representation of extended symmetries beyond the simpler symmetries represented by groups.

#The favorite family of [[../GroupRepresentations/|group representations]] in the current, [[../QuarkAntiquarkPair/|Standard Model of physics]] (called ''[[../SUSY2/|SUSY]]'') is that of the <math>U(1) \times SU(2) \times SU(3)</math> product of symmetry groups; this choice might explain some of the limitations encountered in [[../SUSY4/|High energy physics]] using SUSY and the corresponding physical representations of the symmetry associated with this product of groups, rather than ''[[../WeakHopfAlgebra/|quantum groupoid]]''-related symmetries. It is also interesting that ''[[../NoncommutativeGeometry4/|noncommutative geometry]]'' models of [[../LQG2/|quantum gravity]] seem also to be `consistent with SUSY' (''viz.''  A. Connes, 2004).

#The quantum treatment of gravitational fields leads to [[../TopologicalOrder2/|extended quantum symmetries]]
(called ''`supersymmetry''' ) that require mathematical representations of [[../HamiltonianAlgebroid3/|superfields]] in terms of
''graded `[[../BilinearMap/|Lie' algebras]]'', or ''[[../AntiCommutationRelations/|Lie superalgebras]]'' (Weinberg, 2004 <ref name='SW2k4'/>).

#Simplified mathematical models of networks of interacting living cells were recently formulated
in terms of ''symmetry groupoid representations'' , and several interesting [[../Formula/|theorems]] were proven for such
[[../TrivialGroupoid/|topological structures]] (Stewart, 2007) that are relevant to relational and functional biology.

Several areas of functional biology, such as: \emph{functional genomics, interactomics,
and [[../SupercomputerArchitercture/|computer]] modeling} of the physiological functions in living organisms, including humans
are now being developed very rapidly because of the huge impact of mathematical representations
and ultra-fast numerical [[../LQG2/|computations]] in medicine, biotechnology and all life sciences.
Thus, biomathematical and bioinformatics approaches to functional biology
utilize a wide range of mathematical concepts, theories and tools, from ODE's to biostatistics,
probability theory, graph theory, topology, [[../PAdicMeasure/|abstract algebra]], set theory, algebraic topology, categories,
[[../LM_nLogicAlgebra/|many-valued logic]] algebras, [[../InfinityGroupoid/|higher dimensional algebra]] ([[../2Groupoid2/|HDA]]) and [[../SuperCategory6/|organismic supercategories]].
Without such mathematical approaches and the use of ultra-fast computers, the recent completion of the first
Human genome projects would not have been possible, because it would have taken much longer and
would have been far more costly.

==All Sources==
<ref name='RMcW2k2'/>
<ref name='NR62'/>
<ref name='SW2k4'/>
<ref name='NB64'/>

==References==
<references>
<ref name='RMcW2k2'>
R. McWeeney. 2002. ''Symmetry : An Introduction to Group Theory and Its Applications.''
Dover Publications Inc.: Mineola, New York, NY.

</ref><ref name='NR62'>
N. Rashevsky.1962. ''Mathematical Biology'' . Chicago University Press: Chicago.

</ref><ref name='SW2k4'>
S. Weinberg. 2004. ''Quantum Field Theory'' , vol.3. Cambridge University Press: Cambridge, UK.

</ref><ref name='NB64'>
N. Bourbaki. 1964. Alg\`ebre commutative in \'El\'ements de Math\'ematique, Chs. 1-6, Hermann: Paris.

</ref></references>

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