The fundamental importance of the path integral suggests that it might be enlightening to simplify things somewhat by stripping away the knot observable K and studying only the bare partition functions of the theory, considered over arbitrary spacetimes. That is, consider the path integral

Z(M) = ∫ DA e (i ∫_{M} S(A) —– (1)

where M is an arbitrary closed 3d manifold, that is, compact and without boundary, and S[A] is the Chern-Simons action. Immediately one is struck by the fact that, since the action is topological, the number Z(M) associated to M should be a topological invariant of M. This is a remarkably efficient way to produce topological invariants.

Poincaré Conjecture: If M is a closed 3-manifold, whose fundamental group π_{1}(M), and all of whose homology groups H_{i}(M) are equal to those of S^{3}, then M is homeomorphic to S^{3}.

One therefore appreciates the simplicity of the quantum field theory approach to topological invariants, which runs as follows.

- Endow the space with extra geometric structure in the form of a connection (alternatively a field, a section of a line bundle, an embedding map into spacetime)
- Compute a number from this manifold-with-connection (the action)
- Sum over all connections.

This may be viewed as an extension of the general principle in mathematics that one should classify structures by the various kinds of extra structure that can live on them. Indeed, the Chern-Simons Lagrangian was originally introduced in mathematics in precisely this way. Chern-Weil theory provides access to the cohomology groups (that is, topological invariants) of a manifold M by introducing an arbitrary connection A on M, and then associating to A a closed form f(A) (for instance, via the Chern-Simons Lagrangian), whose cohomology class is, remarkably, independent of the original arbitrary choice of connection A. Quantum field theory takes this approach to the extreme by being far more ambitious; it associates to a connection A the actual numerical value of the action (usually obtained by integration over M) – this number certainly depends on the connection, but field theory atones for this by summing over all connections.

Quantum field theory is however, in its path integral manifestation, far more than a mere machine for computing numbers associated with manifolds. There is dynamics involved, for the natural purpose of path integrals is not to calculate bare partition functions such as equation (1), but rather to express the probability amplitude for a given field configuration to evolve into another. Thus one considers a 3d manifold M (spacetime) with boundary components Σ_{1} and Σ_{2} (space), and considers M as the evolution of space from its initial configuration Σ_{1} to its final configuration Σ_{2}:

This is known mathematically as a cobordism from Σ_{1} to Σ_{2}. To a 2d closed manifold Σ we associate the space of fields A(Σ) living on Σ. A physical state Ψ corresponds to a functional on this space of fields. This is the Schrödinger picture of quantum field theory: if A ∈ A(Σ), then Ψ(A) represents the probability that the state known as Ψ will be found in the field A. Such a state evolves with time due to the dynamics of the theory; Ψ(A) → Ψ(A, t). The space of states has a natural basis, which consists of the delta functionals Â – these are the states satisfying ⟨Â|Â′⟩ = δ(A − A′). Any arbitrary state Ψ may be expressed as a superposition of these basis states. The path integral instructs us how to compute the time evolution of states, by first expanding them in the Â basis, and then specifying that the amplitude for a system in the state Â_{1} on the space Σ_{1} to be found in the state Â_{2} on the space Σ_{2} is given by:

〈Â_{2}|U|Â_{1}〉= ∫^{A | ∑2 = A2} _{A | ∑1 = A1} DA e i S[A] —– (2)

This equation is the fundamental formula of quantum field theory: ‘Perform a weighted sum over all possible fields (connections) living on spacetime that restrict to A_{1} and A2 on Σ_{1} and Σ_{2} respectively’. This formula constructs the time evolution operator U associated to the cobordism M.

In this way we see that, at the very heart of quantum mechanics and quantum field theory, is a formula which associates to every space-like manifold Σ a Hilbert space of fields A(Σ), and to every cobordism M from Σ_{1} to Σ_{2} a time evolution operator U(M) : Σ_{1} – Σ_{2}. To specify a quantum field theory is nothing more than to give rules for constructing the Hilbert spaces A(Σ) and the rules (correlation functions) for calculating the time evolution operators U(M). This is precisely the statement that a quantum field theory is a functor from the cobordism category nCob to the category of Hilbert spaces Hilb.

A category C consists of a collection of objects, a collection of arrows f:a → b from any object a to any object b, a rule for composing arrows f:a → b and g : b → c to obtain an arrow g f : a → c, and for each object A an identity arrow 1_{a} : a → a. These must satisfy the associative law f(gh) = (fg)h and the left and right unit laws 1_{a}f = f and f1_{a} = f whenever these composites are defined. In many cases, the objects of a category are best thought of as sets equipped with extra structure, while the morphisms are functions preserving the structure. However, this is neither true for the category of Hilbert spaces nor for the category of cobordisms.

The fundamental idea of category theory is to consider the ‘external’ structure of the arrows between objects instead of the ‘internal’ structure of the objects themselves – that is, the actual elements inside an object – if indeed, an object is a set at all : it need not be, since category theory waives its right to ask questions about what is inside an object, but reserves its right to ask how one object is related to another.

A functor F : C → D from a category C to another category D is a rule which associates to each object a of C an object b of D, and to each arrow f :a → b in C a corresponding arrow F(f): F(a) → F(b) in D. This association must preserve composition and the units, that is, F(fg) = F(f)F(g) and F(1_{a}) = 1_{F(a)}.

1. Set is the category whose objects are sets, and whose arrows are the functions from one set to another.

2. nCob is the category whose objects are closed (n − 1)-dimensional manifolds Σ, and whose arrows M : Σ_{1} → Σ_{2} are cobordisms, that is, n-dimensional manifolds having an input boundary Σ_{1} and an output boundary Σ_{2}.

3. Hilb is the category whose objects are Hilbert spaces and whose arrows are the bounded linear operators from one Hilbert space to another.

The ‘new philosophy’ amounts to the following observation: The last two categories, nCob and Hilb, resemble each other far more than they do the first category, Set! If we loosely regard general relativity or geometry to be represented by nCob, and quantum mechanics to be represented by Hilb, then perhaps many of the difficulties in a theory of quantum gravity, and indeed in quantum mechanics itself, arise due to our silly insistence of thinking of these categories as similar to Set, when in fact the one should be viewed in terms of the other. That is, the notion of points and sets, while mathematically acceptable, might be highly unnatural to the subject at hand!