Does Proof of Existence lose bitcoins? http://www.proofofexistence.com/about -- "Use our service to anonymously and securely store an online distributed proof of existence for any document."


  The document is certified via embedding its SHA256 digest in the bitcoin blockchain. This is done by generating a special bitcoin transaction that encodes/contains the hash via an OP_RETURN script. This is a bitcoin scripting opcode that marks the transaction output as provably unspendable and allows a small amount of data to be inserted, which in our case is the document's hash, plus a marker to identify all of our transactions.


Naïve question perhaps, but if the bitcoins are lost forever, this seems like an unfriendly use of the bitcoin protocol and the blockchain, and future versions of the protocol may prevent this type of transaction from being accepted into the blockchain?
Well, it's probably not an intended function of the block chain, but I wouldn't call it "unfriendly" because you're not really harming anybody (by reducing the total amount of bitcoins available you're in fact increasing the value of all other bitcoins a little).


  [...] future versions of the protocol may prevent this type of transaction
  from being accepted into the blockchain?


No, because it's not possible. The transaction encoding the document hash looks exactly like any other normal pay-to-address transaction. The only difference is the address which is a representation of the document hash instead of a hashed public key, and therefore there is no private key associated with it (that's why it is unspendable). You can't go back from a hash to it's origin though, so you will never know whether it's spendable or not.