The thing I don't think I'm grasping is that--when the bonds form, they produce more energy than they take in, right?
Usually when a bond forms, it doesn't produce energy, it takes in energy. Bond breakage is what releases energy (there are probably exceptions to this but not any we need to worry about here)
So, our puddle--which has a goal of reducing the energy in its system into a non-usable form
There is no goal (as in, no conscious desire for either increased entropy or decreased entropy on the part of the puddle) and/but what happens is that living molecules allow much less energy to be lost to entropy than would otherwise occur, which is why an organized energy increase is favored. (See below for my addendum to this statement, because its not exactly accurate)
I'm not getting something obvious here--I pretty much understand that. I'm just looking for what it is. (I'm going to guess looking at the puddle as a system is myopic because it's not actually closed ect. But the core of it is, if you've got sunlight increasing energy, and this theory states the drive for "life" is to better use that energy up
This is where your error is. The drive for living molecules allows the energy to be converted more efficiently, so less is lost to entropy.
Recently I've been tempted to go back to school for a more STEM oriented degree (Complete the higher end math courses I took, and try for Chem or Phys),
Do both! Dual major in Chem/Phys!
Added: Let me amend what I'm saying a bit. By better organizing the energy, it IS better dissipated, so in that regards, more is lost to entropy over time, but in the process it is being used more efficiently. So when I say that the energy is more organized and therefore less is being lost to entropy, what I mean by that is that the energy that is being injected into the system from outside is goes through more changes and is used for more work before it is lost as entropy.
Think about it like this. The Sun is firing all this energy at this puddle. Now that energy can hang out for a few minutes, and then be lost as heat energy, or molecules can harvest that energy and convert it to work to power their reactions, and then portions of that energy are lost as heat energy or entropy. Which is more efficient in terms of the energy being used for work? The latter. So that's what drives this. The molecules are harvesting the energy and using it, instead of it just being lost to entropy.
Hopefully that better clarifies what I mean.
Here's a copy of Jeremy England's paper on the subject, he being a physicist and in post grad probably can explain it better than I can
http://www.englandlab.com/uploads/7/...013jcpsrep.pdf