042-the cell

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 that has importance in chemistry though.  Cells 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, certain chemical compounds, creating  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 atomic interactions of the molecules.  

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 by atomic level interactions.  

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 the 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 idea in biology.  Biology does not concern itself with physics or chemistry directly, it concerns itself with cells, the biological components of cells, 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 thing per se, it is an idea about a grouping of molecules and their physical interactions. The cell is a way for us 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 physical reality is that physical and chemical interactions are occurring en masse.  

This separation of molecular phenomena into cells is not just our subjective conception, or projection that we make onto chemical and physical phenomena. It is a separation of molecular structures and interactions that the cell itself is making.  The cell separates molecules and physical interactions. The cell is separating molecules and molecular interactions into representational structures and reprsentational functions.  That there are biological structures and biological functions is not a feature of physics or chemistry, it is a feature of representation making.  The cell makes and is made of biological functions and structures separated 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, the same physical and chemical phenomena occur in both situations.  

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, are representation making processes instantiated in the sub-strata of physics.  


The protein

The protein is the predominant representation making process of the cell.  

When we look at chemical phenomena, what happens at the level of individual atoms?  

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