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Curiously, the Moon's center of mass is offset from its geometric center by about 2 km in the direction toward the Earth.Also, the crust is thinner on the near side.
In general the earth's interior has been sorted by Gravity. Heavier elements like iron tend to sink toward the center or core of the earth. Lighter materials, the silicates, oxygen compounds and water have risen to become part of the crust. This action has created distinct layers within the earth and is still in process today.Oceanic crust - The crust under the oceans is about 10 km thick and is generally made up of rock rich in iron and magnesium. These are primarily basalt formed by volcanic action at the mid ocean ridges. The oceanic crust is denser than continental crust.Continental crust (continental cratons) - Where there are continents the crust is about 30 to 50 km thick. It is made up of igneous, metamorphic, and sedimentary rocks. The continental crust is less dense than the oceanic crust. When the continental crust collides with oceanic crust through plate movement the continental crust rides over the top of the oceanic crust while the oceanic crust is pushed back down towards the mantle.
RD is on the right track- igneous rocks fractionate as they cool, that is the heavier minerals that form first sink deeper into the magma chamber, and the lighter, more volatile minerals and elements tend to rise toward the top. For a simplified explanation, check out the Bowen Reaction Series http://en.wikipedia.org/wiki/Bowen's_reaction_seriesLighter rocks would stay at the surface (sort of like foam on water) and eventually coalesce.
Oceanic volcanoes, mid-ocean rifts and rift basalts eject magma that form crust. And there are magma chambers where subduction material returns upward towards the surface of the earth that often break through and form volcanos but also cool under the surface, forming granites and dikes, sills and pagmatites.
But there weren't any oceans when the crust was originally forming.You've mentioned subduction. But if the crust were of uniform density, how could subduction occur? As far as I am aware it is the difference in density between the plates being pushed together that causes subduction.
There is overwhelming evidence for plate tectonics at 3.0 b.y. There is fairly convincing evidence that plate tectonics is at least as old as 4.0 b.y. Analysis of zircon crystals suggest water may have covered the earth as early as 4.3 b.y., and that plate tectonics may have been active at that time.
Even today, subduction occurs at oceanic plate to oceanic plate convergence zones- the crust on each side of the subduction zones should be close to equal density. What causes subduction? There are several hypotheses and not all of them require density differences between plates.
Also, as igneous magmas fractionated, they would create igneous rocks of differing densities- everything from dense peridotite/basalt to relatively light granite.To me, the more intriguing questions involve the difference between the processes we see active today and those that created the ancient cratons- for example, the great archean greenstone belts, of which we have no modern analogues.