When CT is fully implemented in browsers and operating systems alongside pinning, a certificate that doesn't appear in the corresponding CA's certificate-issuing list or that fails a pinning test will give a user a chance to react. CT will also be used by companies like Google and independent security organizations to monitor actively for problematic security documents.
Pinning, and soon certificate transparency, absolutely do not solve all problems related to misuse of certificates. But on their own and together, they reduce the area of potential of harm by making it far harder for a sniffer to obtain a certificate and insert themselves into a secure connection without being immediately caught.
The alerts that browsers will provide will allow users quite legitimately to feel as if they are part of the effort to provide integrity to the Internet's plumbing.
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