Quick google says the average honeybee can fly about 20mph. I’d imagine it would be some combination of air being dragged with the boat, and the bee flying forward resulting in the bee and boat traveling at the same speed. You can see seabirds riding the air pushed forward by larger ships. Same principle
A boat traveling on the surface has some areas around it that are more-or-less protected from the wind. Especially if you’re behind the main deck protrusions (usually some sort of cabin), there will be an area of negative pressure that drags air along with the boat.
Similarly if you’re low in front of protrusion, then the air piles up. Most of the wind goes over this “pile” of air, so if you’re inside of it, there isn’t much wind.
Other than that, if the bee gets out of the lee of the cabin or isn’t in one of those relatively calm areas in front of the cabin, it’ll instantly get blown away by that 40 mph wind rushing over the deck.
A bee flies by applying force on the air with its wings, just like how you swim through water.
When the air (or water) is stationary, you’ll move forward. The air inside an enclosed vehicle with windows closed is stationary, moving at the same speed as the car. The bee can easily get to where it wants to go WITHIN that stationary bubble of air, just as if it were flying around a garden on a calm day.
When the air (or water) is moving, it creates currents that can make movement more difficult. When riding in a boat, the bee can move around the stationary air inside the cabin or, in the open cockpit area, under the column of air flowing up and over the windshield. Fly above that stationary air, though, and the bee will be caught in the current and ejected from the vehicle.
If the bee is in an enclosed cabin, then the air it’s flying in is also moving with the boat. So the bee would be able to hover with the boat just as it would with solid ground.
If the bee is in an open canopy, then the bee will move with the wind surrounding the boat, regardless of the boat’s own speed. So it will only hover with the boat if the boat just happens to have a tailwind as fast as its own speed.
But wind forces aside, Newton’s First Law does dictate that the bee will maintain its original speed until a force is applied to it. If that original speed happens to be that of the boat, then the bee will keep moving at the speed of the boat until another force acts on it. Whether that’s wind, the bee’s own propulsion, or a fly swatter.
A feature of fluid dynamics is that near the solid interface the velocity of the fluid is close to that of the solid (i.e. 0 if the solid is not moving, 40 mph if the solid is moving 40 mph). If the bee is close enough then the “wind” of the blowing air as a result of the moving vehicle won’t be 40 mph.
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