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That elides the fact that if there was such a conspiracy, it would not have been conducted by the government en bloc, but by a subset of the government. A specific task group or department cannot be assumed to suffer from the same kind of porblems that permeate very large institutions.
There is no subset of the U.S. government that is capable of enlisting a dozen or so Islamist extremists and persuading them to carry out suicide attacks on the U.S. So either everything we've learned about the hijackers is wrong, in which case not only the entire U.S. intelligence apparatus but also that of several other countries is in on the conspiracy, or there was no conspiracy.
The idea also makes no sense. If you wanted to terrify the U.S. population into accepting authoritarian measures (real ones, not the stuff in the Patriot Act), you would launch a series of dramatic attacks. If you wanted to invade Iraq, you'd create plausible links between the attackers and Iraq. Neither one is what happened. I conclude that this idea is strictly loony tunes.
The idea that there is a conspiracy to wipe out microbiologists, epidemiologists and protein chemists is almost as implausible. I have no trouble believing that a particular scientist working on bioweapons might be killed for some reason (though I would think the prior probability would be low), nor do I have trouble believing that someone might carry out biowarfare experiments on the public (though again the probability that any particular outbreak of illness is such an experiment is low). A wide-spread conspiracy is a different matter. I can't formulate a plausible hypothesis for a group that would have both the motivation and the capability of carrying out such a conspiracy. And why protein chemists, for goodness sake?
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