047-Systems Biology

Uri Alon's Introduction to Systems Biology and the lectures available on youtube https://www.youtube.com/watch?v=Z__BHVFP0Lk are excellent resources to understand how networks of molecular interaction produce representational action.  The current approach focuses on the mathematical nature of these interactions.  But for our purposes, what is important is every interaction.  The representations themselves are what matter.  While it is aggregate interactions which guide cellular behavior, for representational purposes, ever interaction matters.  

If we think of systems biology processes as representational networks, we can see how quantities of molecules and steady states of molecules, decay rates, and molecular constructions work together to produce representation.  The representations are meaningful to the cell, and we naturally refer to the cells behavior as aware behavior, but the awareness of the cell is limited, at best, to the context of representation making the cell engages in.  

If we want to impart awareness into the cell, it is best to impart it into the signaling pathway structures the molecular interactions create and not at the edge of the interaction at the inputs and outputs.  The problem with imparting actual awareness to the cell is the problem of what the cell is aware of?   If we say the cell is aware of a toxin or aware of a food source, what is the thing the cell is aware of?  A molecule that initiates a reaction in the biological networks of the cell.  So where is the awareness?  Where is the representation of an awareness kept by the cell?  And there is none. 

The molecular interaction network structures of systems biology are functionally little different from other kinds of networks.  But what we see at the level of the biological chemistry is there is no duality.  If we say the cell is aware of some food source, what we mean is that some molecule has initiated a cellular systems network that causes the flagella to rotate in such a way as to guide the cell to that food source.  The cell is not aware of food, as quale, or even as "food".  Rather, there is a causal chain of interaction from "food" molecule to cellular network activity to directed action to "food" source.  The cell is not aware of food.  

What the cell is aware of, if the cell is aware at all, would be it's internal representations.  And those exist only as the network of molecular interactions.  So the awareness of a cell is very different from our awareness.  The cell has no memory per se, rather, the cell has an instantiated network of representations for it's world, a sort of constant simulation of the moment of it's world.  

And that is the key feature.  The cell has molecular networks that serve as a simulation of it's world.  A molecule which is actually toxic may trigger a network that treats that molecule as a nutrient source and moves to the toxic molecule.  Like us, the cell does not really know anything about the world it inhabits, what it knows, or knows to do, is respond to the simulation generated by it's molecular interaction networks. 

As we will see later, the kinds of representations molecular interaction networks can create are limited.  
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