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In essence you characterize the Qaeda attacks as a hack, in the computer security sense. That's an excellent analogy — as writers like Salon's Patrick Smith and others have observed, the attackers exploited a mindset rather than a particular security hole.
And if the September 2001 attacks were the only ones of their kind, that would probably be as far as anyone needed to think about them. But they weren't. Al Qaeda had been making plans to infiltrate the US in numbers, and coordinate the hijacking and crashing of multiple planes, for years before 2001 — and been caught every time.
Suppose you were brought in as a consultant to do a postmortem on a data security breach, and you discovered that the exploit in question had actually been patched as late as a few months before the intrusion — but the patch had somehow been uninstalled since then.
If you ask yourself the question: "who benefits?", and you ask it honestly, then the answer must be Islamic extremists.
It's hard to look at the last 7 years and accept that the Bush regime did not also benefit in any way from the World Trade Center attacks.
At the risk of stretching my analogy, suppose that the in-house security guy tells you that there was no way of knowing about the exploit, and refused to answer any questions about how the patch that used to be there had been removed — or whether there was any connection to the huge budget increase and sweeping new authority he was demanding to fight future intrusions.
At the very least, you'd have to consider the possibility that he was grossly negligent and attempting, with breathtaking audacity, to turn his own fuckup into an opportunity for self-advancement.
And you'd have to at least think about whether he'd been willfully negligent.