Anatomy of a Fire

I currently stay with a chemistry grad student. He occasionally starts a fire pit in the back. Somehow, we got to pontificating on why fire looks the way it does. I thought to synthesize his hunches because: 1. they sounded right 2. i have no reason to doubt a phd chemist 3. it sounded cool

Basically wood is a solid fuel. It's packed densely with cellulose (amongst other sugar chains and other long chain molecules). Heat liberates these sugars (along with other molecules). As the heat increases, the sugars themselves decompose into alcohols. The liberated decomposed sugars and other molecules become a gas. What we observe as the flames of the fire is oxidation of this heated gas. The escaping gas ignites under heat and oxygen, giving the fire its characteristic flicker. The light and heat we feel from a fire is actually the radiation from this oxidation reaction. Some of liberated radiation in the visual spectrum (the light of the fire). A lot of the heat we feel from the fire is radiation released in the IR spectrum.

The flame persists for a while because the fire is a self-catalyzing reaction. The radiation released from the oxidation reaction becomes the heat that's used to liberate more molecules from the wood. This creates more gas. New oxygen diffuses in and reacts with the heated gas -- releasing even more energy that's again used to liberate more gas. This is why fanning flames sometimes help fires catch. When you fan, you blow away the gas and replace it with a bunch of oxygen. So when you stop fanning, there's a lot of oxygen for the gas to react with. But it's also important not to fan too much. You run the risk of decreasing the temperature of the reaction zone above the wood.

The embers of charcoal that are left glowing is actually extremely hot carbon remnants of the wood. The heat and light we see from charcoal is actually blackbody radiation. You'll notice if you pick up what's left from a fire, the wood is considerably less dense. Basically, the solid sugar fuel for the fire burned up, leaving the carbon shell of what held the fuel. This carbon shell itself glows when its hot. The charcoal you buy in a store is basically this stuff ground down to a dust and pressed together with clay.

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!