Can you give me a link, because I don't know what your getting confused with. There is no such thing as a physics slot, there are only AGP, PCI and PCI-e slots, on up to date motherboards anyways.
I imagine he is referring to the third x16 PCIe connector on motherboards like the Intel BadAxe2.
Motherboards like this were designed at a time when Nvidia and ATI were both making a big song and dance about the possibility of using video cards to do physics calculations. The idea was that high-end gamers would want to use two video cards in Crossfire/SLI mode, plus a third one in the third slot that did Physics and nothing else.
Hardware-assisted physics (performed either by a graphics chip or a dedicated physics card such as the one from Ageia) seems to be going out of fashion at the moment - a shame, as a well-designed physics processor could easily be 10 or 20 times as fast as a quad-core CPU.
I suspect it's a "chicken-and-egg" problem: hardly anyone owns a physics card, so there's no incentive for games developers to make games that are compatible with Physics cards; that means there are no physics-accelerated games; that means that there's no incentive for anyone to buy a physics card.
There was a similar problem in the early days of 3D-accelerated graphics, but with 3D there was a way through: you could have exactly the same game, same gameplay, same things happening, and just make it look much, much better if you were using 3D hardware. By contrast it's
impossible to have "low physics" and "high physics" versions of the same game, because the physics affects the behaviour of all of the objects in the game: with acceleration and without acceleration are two completely different games, which is far more complicated to balance and maintain.
That means that a game designed to run adequately without physics acceleration can never be
significantly different or better when it
is using accelerated physics: you're limited to one or two graphically pretty "special effects" sequences, but never anything that actually affects the gameplay.
It's probably also a lack of power in the GPU department. If a game is using accelerated physics the number of objects on screen can be
enormously much bigger than the number of objects in any current game; but if you ask the CPU and GPU to actually render that scene on the screen, everything grinds to a halt, because they simply can't draw 3D scenes as complex as that at acceptable speeds. The result is that, when you add accelerated physics to a game, the game tends to look much better but run much
slower, which gamers don't like. For accelerated physics to be useful you need to havea lot of CPU and GPU capacity to spare.