It is enough to show that the intersection of two finitely generated semigroups inside a finitely generated commutative semigroup is not necessarily finitely generated, for then you can consider the semigroup algebras.
So let be freely generated by subject to the relations and for all , and for all (notice that in fact coincides with the given set of generators...). Let be the subsemigroup generated by and , and let be the subsemigroup generated by and . Then , and are finitely generated and commutative, yet the intersection is the subsemigroup of generated by , which is isomorphic to under the product. This is not finitely generated.
Later: Yemon asks in a comment if one can change this so that the containing algebra is a domain. I think this works: let be the algebra generated by subject to the relations and for all , and for all , let be generated by and , and let be generated by , and . (I have to remove for otherwise )
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