The Turing Problem and Theoretical Biology

Radiolab had an interesting show on Alan Turning. This was really cool because it was the first time I had heard someone describe why Turning machines were so important in a way I could understand.

The idea was to prove there was a machine capable of doing things all the same things a human could do: think, logic, reason, be creative, etc. He got to the point where he could prove a machine that could add, add, subtract, do calculus, and solve mathematical proofs. They did a number of things that, until then, people imagined could only be done by humans. And remarkably, these machines had *very* simple operating principles.

This made me think --

1. Alan is essentially asking the question: can we make machines that think? Origins of life research asks: can we make a cell that replicates?  Perhaps in the same way Alan can show that there is a machine with simple rules that can do extremely sophisticated logic. We can show that a machine with a particular set of rules that replicate.
2. With the rules we identify in point 1, we might be able to identify a molecular state space. These molecular state spaces would be the chemical manifestations of the rules we identify in point 1. To be clear, let me provide an example: Imagine that one of the rules is that cells need a way to store information. Our molecular state space would...
1. Contain all the molecules that we know in biology that carry information (e.g. DNA, RNA)
2. Ideally have its own set of rules themselves that explain why this molecular state space is the solution to the information problem (e.g. Why don't we expect to see information carried in anything except DNA, RNA, or whatever)
3. The purview of synthetic biology would be to take the insights of points 1 and 2 and begin to make autonomous replicating cells.
4. If the program of synthetic biology succeeds -- the only gap to bridge would be thinking about why cells in their particular forms emerged on Earth, or from what they emerged. We'd know what we need to look for in order to *get* to a cell -- right now we have bits and pieces of what we think might work.

Haha, woooooo radiolab!

pH

So I was thinking about pH today and realized why water was so important in defining the scale. It isn't just that water neutral between different Bronsted-Lowry Acids. pH is defined by water.

Water is the simplest molecule with both H and OH and acts as the solvent for most mixtures. We know that pH varies from 0 to 14. That means that water can, at most, accommodate 1 Mol of Hydrogen atoms (pH 0). It has a maximum hydrogen carrying capacity (H3O+ max -- this is most acidic).  Measuring a pH gives a sense of how much the solute is stressing or alleviating water hydrogen carrying capacity.

Conversely, in a basic solution there must be at least least .00000000000001 M (13 zeros) of water  -- for if there were fewer, there would be an enormous stress in the solution to create more. You can make them from all the excess OH floating around.

So pH is a way to thing about how much stress is being put on the water to hold extra hydrogen atoms. But you can imagine that these carrying capacities vary between solvents. That the same solute will have different pHs in different solvents. Ethanol has its own hydrogen carrying capacity which will influence the solute's acidity or alkalinity. In fact, something that's acidic in water can be basic in ethanol.

An interesting and clear explanation of all these ideas are here.

It makes sense then how acid and base equilibrium constants are defined. Acid equilibrium constant is concerned with the acid's capacity to add H to water (you see the solute on right with water and its products are the acidified water and conjugate base). The opposite is true for the base equilibrium constant (you see the basic solute and water on the reactant side and on the product side you see the conjugate acid and what's left of the water molecule).