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The Jones polynomial of a knot in 3-space is a Laurent polynomial in q, with integer coefficients. Many people have pondered why this is so, and what a proper generalization of the Jones polynomial for knots in other closed 3-manifolds is. Our paper centers around this question. After reviewing several existing definitions of the Jones polynomial, we argue that the Jones polynomial is really an analytic function, in the sense of Habiro. Using this, we extend the holonomicity properties of the colored Jones function of a knot in 3-space to the case of a knot in an integer homology sphere, and we formulate an analogue of the AJ Conjecture. Our main tools are various integrality properties of topological quantum field theory invariants of links in 3-manifolds, manifested in Habiro's work on the colored Jones function.
We give a new algorithm to compute inhomogeneous difference equations for a definite sum with parameters. The algorithm is based on the restriction algorithm for D-module by Oaku. Main tool in the algorithm is Gröbner basis method in the ring of differential operators.