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I'd guess they'll continue in cargo service for many more years, just as the DC10 and MD11 did (despite the grounding after the Louisville crash, I expect they will fly again before finally being retired).
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Yes. There are recently built 747-8's that will in service for a couple more decades.
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Fedex continues to fly the MD11; UPS retired their fleet.
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> Top floor existed at all because it was Boeing's entry for a heavy cargo plane competition

Yes, but it turns out the hump is great for area ruling (aerodynamic drag reduction at transonic speeds), as observed by the 747-300's extended hump giving lower drag (but higher weight, of course) than the short-hump versions.

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I think the top floor is there because the crew cabin has to be high so the nose can swing up. The cables and wiring from the cabin can't be easily disconnected to allow such access. You will notice other large cargo variants of airliners load cargo only through the side of the fuselage.
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Yes and no. The C5 has an upper level too. The whole setup solves a lot of problems at once. Opening nose makes for faster cargo operations which the military cares about for a bunch of reasons. There are usually people associated with military cargo so might as well seat them up there.
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I understand that for the 747, they initially just had a cockpit bulge atop the fuselage. However, this created too much drag, which they reduced by extending the bulge aft. They didn't need this space for flight operations, so it was naturally then used for additional passenger space.
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Any large cargo aircraft has primary loading inline with centerline, side doors just aren't efficient. It's either via front, via rear or both.

Me321/323 was I think first heavy cargo with nose clamshell doors, but after that everyone settled on nose rising up, clamshell rear. It also had the top deck.

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