Certificate Transparency has one glaring issue. The Merkel tree proofs can only prove a certificate is present (not that it is absent). The current proposal doe

Certificate Transparency has one glaring issue. The Merkel tree proofs can only prove a certificate is present (not that it is absent). The current proposal does not require "examiners" of the Merkle tree to be provided with the entire contents of the Merkle tree. This means blank check certificates can be issued to governments and companies, be validated and not be detected unless we catch their use in the act. The whole idea of using a Merkle tree to "save energy" is a bit of a sham. The tree produced is imbalanced and will contain a chain of O(N) hashes to validate a certificate, which is the same cost as a signed block chain system (no proof of work).