>I recognize that Starfleet doesn't believe it's purpose is to fight
>wars. However, you build a craft that has shields, miliary grade
>weapons, teach all your captains how to fight, have a security staff,
>and in general treat your crews with military discipline, you have a
>military force.

Starfleet is a military force in all ways except for focus and name. Its officers all have some degree of scientific knowledge; that's demonstrated time and again. (The qualifications just to get into the Academy, as demonstrated in the episode where Wesley took his exam, are downright brutal by modern standards, and probably still high by the 24th century.) The captains and other senior officers of its vessels are typically trained in things like diplomacy and xenomedicine to make forming relationships with new political entities easier, and more benificial.

The UFP is well aware that, in times of war, Starfleet is its military force. And even dedicated science/exploration vessels (such as the Nova-class, which is based on the Defiant project's pathfinder ship -- just pick up the DS9 tech reference and you'll see the resemblance) carry weapons and shields for the purposes of self-defense; after all, one never knows when one might meet a hostile force.

And, I might add, it would appear that Starfleet does field fighters, of a sort: the Peregrine-class appears to be a heavily-armed (for its size) single-pilot craft. (Of course, it's still somewhere around 60' long, give or take, so it's probably got a transporter, head, and sleeping cabin, just like most TNG-era designs.)

-- Sean --

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