Cells are functional ideas - cells do representational actions:

In physics or in chemistry, what is a cell?  A cell is just some molecules.  chemistry does't talk about cells, because cells are just some molecules.  outside the cells are molecules, the cell wall itself is molecules, inside the cell wall, more molecules.  what is a cell wall to chemistry?  nothing but a grouping of certain molecules.

certain chemical reactions in the cell wall will cause the wall to unbind and then the cell itself will disintegrate.  The cell wall is what separates and groups different molecules into a structure we call a cell.  But from the perspective of chemistry, there is no such thing as a cell wall.  It's all just molecules. certainly the molecules have structures, but there is no meaning in the separation of molecules into structures and groups, into "cells".  This separation does serve a function in chemistry.  Membranes separate molecules and restrict their chemical interactions.   

Molecular interactions are the result of the electromagnetic structure and interaction between each atom of each molecule.  The physics of chemical interactions result in creating molecules in certain arrangements, into structures of atoms.  There isn't any cell at all in physics.  All the behavior can be (theoretically) described atomically and from the molecules on up.  Cells are objects in physics, but they are simply structured collections of molecules.  The structure is derived from the electro-magnetic interactions of each atom in a molecule.  

We may refer to cells when discussing physics, but that is only to refer to that structured collection of atoms and molecules, not because the cell is some object which has effects, or produces phenomena in physics.  The cell is an observable phenomena of physics, it is a phenomena produced from atom level interactions of molecules.  

Stars are another example of structured collection of atoms.  We think of the sun, our star, as this thing at the center of our solar system that exerts effects on our planet and solar system..  That is a kind of lay person description.  There aren't particular "sun" physics different from the physics going on elsewhere.  The phenomena we see in the sun are different than at your desk, but the physics are the same.  The physics are the interaction of atoms and sub-atomic particles.  The phenomena of the sun are not products of the sun, they are products of atomic and subatomic interactions.  The sun is a way to refer to some group of atoms producing phenomena such as light, but the sun, is not a thing itself in physics  

When physicists talk about the sun, it's as a description of a collection of atoms that have certain kinds of interactions.  The sun is not a thing that produces effects in physics, it is the interaction of atoms and subatomic particles the creates the effect we call the sun.  At best, the sun, as an object itself, is a side-effect of physical interactions.  For instance, some objects that are part of the physical sun object are the corona, the heliosphere, solar wind, and the heliospheric current sheet.  And if we exclude those objects as being part of the sun, then why should we include the surface, or the core.  All of these are phenomena, or side-effects, that we see from the interaction of atoms.  We could describe the solar system as a kind of cell, whose wall (the heliosphere) is made by the sun.  We don't describe the solar system this way because it doesn't help us to understand the physical phenomena of that object we call the sun.  

If cells are not objects of physics and cells are not objects of chemistry, why do we talk about cells?  Because of biology.  The cell is the basic structure and concept in biology.  Biology does not concern itself with physics or chemistry directly, it concerns itself with cells, the biological components of cells, and with organs, and with organisms.  Biology concerns itself with life.  

But let's be clear about what this means: the cell is not a physical or chemical process which produces physical phenomena.  All of the physical phenomena we see that are produced by organisms and cells are actually the result of chemical and physical processes directly.  There are no biological phenomena, there are chemical and physical phenomena which we categorize as biological. 

The cell is not a physical thing per se, it is an idea about a grouping of molecules and their physical interactions. The cell is a way  to separate and distinguish molecules and molecular interactions,  It is this separation which we assign importance too. This separation is not a physical or chemical phenomena.  What separates cells are molecules too.  There is no molecular separation, there is no physical separation or distinction of the molecules that are cell and non cell molecules.  The separation is a representation.  The separation of different molecular interactions is an idea.  The cell is a representation, and a representational way, to separate and distinguish molecular interactions and phenomena.  The underlying physical reality is that physical and chemical interactions are occurring en masse all the time.  Some of the interactions seem to group together into structures we call cells.  

This separation of molecular phenomena into cells is not only a subjective conception, or projection that we make onto chemical and physical phenomena. The cell is a separation of molecular structures and interactions that the cell itself is making.  The cell separates molecules and physical interactions using the molecular interactions themselves. The cell is separating molecules and molecular interactions into structures and representational functions.  That there are biological structures and biological functions is not a feature of physics or chemistry, it is a feature of the representation making of the cell.  The cell makes and is made of functions and structures that separates itself from the surrounding profusion of physics and chemistry.

There simply are not cells in chemistry and physics. Yet we are made of cells. We have organs. We have bodies.  We interact with organisms. The shift from physics and chemistry to biology is not a change in physics or chemistry.  There is no emergent property called "cells" that are produced by physics or chemical interactions.  Cells or no cells is irrelevant to the occurrence of physical and chemical phenomena.  

The shift to biology is the connection of the representational and the non-representational.  The physics and chemistry are non-represenational.  The cell and biology are representations.  The cell has representational functions..  Multicellular organisms have representational functions and make representations.  Representation making processes are instantiated in the non-representational sub-strata of physics and embodied by the cell. 


Representations take the form x;y or (x y) ; z  or (x y) -> z    Representations which are functional " ->" are different than representations which are identities.   eg.  x = x;y   or  x = x of (x y);z  

"(a b) -> ab"   is a functional representation and this kind of representation is functionally the same as what happens in molecular interactions. "a;b" is a representational idea and this association occurs in networks of cells where the cells reflect the nature "state" of other groups of cells.  

The protein is the predominant representation making process of the cell.  The proteins are enzymes which catalyze chemical reactions vital to metabolism and homeostasis.  In addition to a proteins catalytic functions,  proteins serve mechanical processes through actin and myosin in muscle cells. Proteins also form the cytoskeleton through the formation of microtubules such as tubulin.  Proteins also form structures of the cellular wall. 

The basic form of protein interaction follows the same process as representational transformation with the restriction that all the atomic components of any transformation must be conserved.   

(P mc) -> Pmc          A protein "P"  bonds to some molecule "mc"   
Pmc                         The binding of "Pmc" is unstable and some change to the structure of "P" is induced by this bonding.
Pmc ->  (Pm c) ->  Pm, c          the instability of "Pmc" and the change to Pmc causes "c" to be split from "Pmc"
Pm                          "Pm" is also unstable and the structure of "Pm" will also change,
Pm -> (P m) -> P m          The instability of "Pm" causes a bond change which splits "m" from "P"  The split causes P to takes it's original shape because of the changes in bonding. 

But why should atoms and molecules engage in this kind of process?  Because, that is what they do, driven by the subatomic forces to which they are subject, primarily the interaction of charge relationship of protons and electrons.   For our purposes, why these conformational and binding processes happen is less important than that they happen.  except that the reason these chemical reactions happen is intrinsic to the molecules themselves, and not some extrinsic force that impels, controls, or programs the interaction from afar. 

If we accept that these reactions in this way, and that similar kinds of reactions happen in similar, representational ways, then the problem of constructing representational functions is one of collecting or producing all kinds of molecules to instantiate all kinds representational functions.   

Individually, these chemical reactions serve no representational purpose.  But by collecting these chemical reactions into groups, then these groups of chemical interactions could engage in representation like behaviors.  It is only when the mass of chemical reactions can be contained and then act in a self sustaining way to maintain that containment that we would get some sort of physical process which is has representational functions.  

The fact of a self sustaining group of molecular interactions maintaining their chemical interaction is what a cell does, that is homeostasis.  To achieve this feat in the molecular environment at large, the group of molecules must contain themselves and construct and/or maintain a membrane.  It is the self-sustaining molecular interactions enclosed by a membrane which is the cell.  The key problem of the cell is homeostatic function.   

A cell faces many kinds of environmental conditions which would destroy it's ability to be self sustaining will survive better if it has mechanism by which to alter and manage the molecular interactions of it's interior, but also to interact with the environment at large and regulate it's membrane.   But these challenges of homeostatic maintenance are not physical challenges.  From the perspective of physics and chemistry, whether a group of molecular interactions is self sustaining or not, or enclosed in a membrane or not is irrelevant.  The physics is non-representational.  The idea of homeostasis, of enclosure, of self-sustaining are just that, representations.   Physical processes which become cells are instantiate the representational imperative to homeostasis.  

The fact of cellular existence is the instantiating fact of representation formation.  Cells embody representational functions.  Examples of representational functions are avoid, seek, grow, divide, wait.