You give the same protein sequence to multiple miners, and the one with the minimum energy after time X wins the money. This will force the miners to find lowest energy solutions.
The way our coin helps is by convincing the mass amount of computational power that is dumped into altcoins that will eventually fade away, or become scam coins, to be better used towards something that will benefit the world.
The BTC miners i do not believe waste energy as they are providing a fantastic transaction ledger.
Counterparty is really innovative, and this is a great way to leverage it. Unfortunately, it's really easy to confuse with typical altcoins which really use miners.
This is great because it allows our development team to work on features, rather than a blockchain and wallet system that can be very hard for a small team of 5 to maintain. Please read this page if you havent already about the pros and cons of Counterparty http://foldingcoin.net/fldc-vs-alts/