Re-examinated patents are still valid?

In “Patenting the obvious?” (pdf), you’ll read about people fighting against a patent on methods for making embryonic stem cells from primates. I won’t go into the details about the patent in itself (although I think that there shouldn’t be any patent based on or containing living “things” or part of it). I just want to share my surprise when I read this (emphasis is mine):

In its 2 April statement, the patent office said that it accepted these arguments, and intended to revoke the patents. WARF has until June to respond to the decision, and if it is unhappy with the outcome, it can then initiate an appeal. The patents will be treated as valid until the re-examination process is complete — that is, until WARF’s response and the possible appeal have concluded. That could take years.

In other words, you can fill as many patents as you want, even if they are stupid, even if you don’t disclose prior art (making your patent irrelevant): even if your patent is challenged, it will be valid for years! How is it possible?

I’m not a lawyer but I looked for details about the classical appeal procedure … Let’s say 2 people enter the court, one as a defendant and the other as a plaintiff. Both are supposed innocent. After the trial, if the settlement does not please one of the parties, one can fill a notice of appeal and the whole thing will be heard by the next higher court with jurisdiction over the matter. During the appeal, both parties remain presumed innocent! It is like nothing happened and everything has to start again. Apparently, in the US Patent and Trademark Office, it’s not the case: once they took a decision, it cannot be changed until the end of all appeal. I think this is also wrong.