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In-Q-Tel, the venture arm of the Central Intelligence Agency with an office here in Silicon Valley, has now lost three managing general partners over the past year.

However, this does not surprise us. It is just like any other government-related investment agency. Like CalPERS here in California, there is a steady stream of departures among top investment managers. If managers are any good, they get sucked up by the private sector, which pays more. It is the way the system works.

Some people are saying the defections point to “some very real problems” at In-Q-Tel, and shrug off suggestions they are merely compensation related. However, we’re not so certain.

Here is what we know: Mark Frantz, a managing general partner at In-Q-Tel has just left to become general partner with Reston, VA’s Redshift Ventures, formerly known as SpaceVest.

His departure follows that of Gilman Louie, who left early this year to launch a new firm here in Silicon Valley with Stewart Alsop. Louie, who was chief of In-Q-Tel, and quite respected, left to make more cash, according to his partner Stewart Alsop. Yes, he made a decent $800,000 income, but that’s nothing compared to what Alsop thinks Louie can make outside of the government contracted entity.

Finally, Amit Yoran, who replaced Louie left just a few months later to “spend more time with his family,” which is the official line In-Q-Tel trots out for any such resignation (the same line was used when Louie departed, just two days before he popped up in the venture with Alsop, which had been in the works for some time). But three months in the job doesn’t really tell us whether there any real problems at In-Q-Tel. In fact, it may say more about Yoran than In-Q-Tel.

At the end of the day, though, we don’t know. It is just that until now, we’ve been surprised that In-Q-Tel had been doing as well as it has — linking up with top-tier venture firms to invest in key intelligence technologies. So we’re not jumping to conclusions.