Earlier quoted context omitted.
"After all, scientifically speaking, everything beyond our sensory nerve-endings is latent and is inferred." This is not a scientific claim, it is a philosophical one, and a dubious one at that ( http://plato.stanford.edu/entries/sense-data/ ).
You don't seem to understand. I wasn't making a philosophy-of-mind claim about philosophical sense-data. I was making a claim, a very basic claim, in neuroscience. In some theories, the nerves don't even pass unaltered signals up to the brain! Everything beyond the sensory nerve-ending itself may involve some amount of inference, inferences performed in the spinal cord and sensorimotor cortex themselves long before a…
Science doesn't operate from the first person perspective. The data of science is not neural firings, it is public observations and measurements.
The sense in which a subatomic particle is inferred from its effects is completely different from the sense in which the brain "infers" things based on neural signals. The former is part of theorizing, the second is a bit of information processing that's prior to theorizing of any kind. The former is a fact about how science works. The latter is a scientific discovery which does not (directly[0]) affect how we do science.
[0] I say directly because there are contexts where we have to account for bias, optical illusions, and whatnot. It's the same sense in which astronomy is not directly about telescopes, though astronomers spend a lot of time worrying about telescopes.