If you submerge a bottle of water in a boiling pot of water, why doesn't the water inside the bottle start to boil as well? I put a glass bottle in a big pot, bottleneck up, I fill both pot and bottle with very hot water. 
The bottle is submerged except a few  cm of the bottleneck and filled to the brim so some water inside the bottle is above the pot water.
Then I light the fire. After a while the water in the pot boils but even if I keep it boiling for 30 minutes the water inside the bottle does not boil.
All I see in the water inside the bottle are very tiny bubbles.
The same happens if I put the bottle upside down (with some air at the top)
What is the reason? 
Maybe the glass acts as insulator and water inside the bottle cannot reach 100 degrees? 
Or having a few cm of bottle (and water) above the pot surface cools the water inside?
 A: To figure out why this happens, you need to think about what boiling is, and how it works.
As you would know, the water in the pot boils because its temperature was raised above the boiling point by the flame. This required a net transfer of heat from the flame, through the pot, to the water in the pot. Why did the heat flow in this direction? Because the flame is hotter than the water in the pot, even when the water starts boiling ($T_{flame} > T_{boil}$)
Now, think about the water in the bottle. The only way for it to get heat is through the water in the pot. As long as the temperature of the water in the pot, $T_{pot}$, is less than $T_{boil}$, it is still liquid, and it transfers some heat to the water in the bottle. The water in the pot boils off at $T_{boil}$, and can no longer transfer heat as efficiently to the water in the bottle. 
This effectively means that the water in the bottle is restricted to a maximum temperature of slightly less than $T_{boil}$, and that is why it never boils.
Another way to think of this is, there must be a temperature difference for a heat transfer to take place. Since the maximum possible temperature of the pot water is $T_{boil}$, the temperature of the bottle water can never exceed this.
EDIT: Another factor to consider is the low conductivity of glass, which means a high temperature difference is required to let a small heat flux through.
A: This just demonstrates that the water is cooler than 100C. It boils only because it is in touch with the bottom, which can be hotter than 100C. But, the rest of the pot's surface is is much cooler and the content (the water) is a continous gradient of temperature drop from hot bottom to the cool walls and roof (do you use the lid?) 

The picture from http://microondeeultrasuoni.wordpress.com demonstrates how your "bottle" does floats above the 100C bottom. What do you want boiling at that, lower, temperature?
A: When water boils if first heats up to 212, warming at a rate of so many degrees per so many BTUs. But when it hits 212 it slows down. A ton more heat energy goes into the water without it increasing in temp. The extra energy is building up to a PHASE CHANGE. I forget the amount required, but there's a several minute pause while it gets ready to change to steam. It accumulates the extra energy without changing temperature. It's changing phase instead. Finally the water molecules have accumulated enough energy to jump free of the pot.
So the second pot can easily heat up to 212 because the water in the first pot is 212, but it can't get to the phase change, it can't reach the boiling stage because the water in contact with it on other side of the glass will never exceed 212; the extra energy from the burner is being captured by the first water, changing it to steam. The second pot is in effect "blocked." 
